diff --git a/src/core/services/cli-command.test.ts b/src/core/services/cli-command.test.ts
index 76563a5..3935d24 100644
--- a/src/core/services/cli-command.test.ts
+++ b/src/core/services/cli-command.test.ts
@@ -220,6 +220,18 @@ test('handleCliCommand processes --start for second-instance when overlay runtim
   );
 });
 
+test('handleCliCommand applies cli log level for second-instance commands', () => {
+  const { deps, calls } = createDeps({
+    setLogLevel: (level) => {
+      calls.push(`setLogLevel:${level}`);
+    },
+  });
+
+  handleCliCommand(makeArgs({ start: true, logLevel: 'debug' }), 'second-instance', deps);
+
+  assert.ok(calls.includes('setLogLevel:debug'));
+});
+
 test('handleCliCommand runs texthooker flow with browser open', () => {
   const { deps, calls } = createDeps();
   const args = makeArgs({ texthooker: true });
diff --git a/src/core/services/cli-command.ts b/src/core/services/cli-command.ts
index ff22bfd..0d2ec35 100644
--- a/src/core/services/cli-command.ts
+++ b/src/core/services/cli-command.ts
@@ -1,6 +1,7 @@
 import { CliArgs, CliCommandSource, commandNeedsOverlayRuntime } from '../../cli/args';
 
 export interface CliCommandServiceDeps {
+  setLogLevel?: (level: NonNullable<CliArgs['logLevel']>) => void;
   getMpvSocketPath: () => string;
   setMpvSocketPath: (socketPath: string) => void;
   setMpvClientSocketPath: (socketPath: string) => void;
@@ -127,6 +128,7 @@ interface AppCliRuntime {
 }
 
 export interface CliCommandDepsRuntimeOptions {
+  setLogLevel?: (level: NonNullable<CliArgs['logLevel']>) => void;
   mpv: MpvCliRuntime;
   texthooker: TexthookerCliRuntime;
   overlay: OverlayCliRuntime;
@@ -149,6 +151,7 @@ export function createCliCommandDepsRuntime(
   options: CliCommandDepsRuntimeOptions,
 ): CliCommandServiceDeps {
   return {
+    setLogLevel: options.setLogLevel,
     getMpvSocketPath: options.mpv.getSocketPath,
     setMpvSocketPath: options.mpv.setSocketPath,
     setMpvClientSocketPath: (socketPath) => {
@@ -232,6 +235,10 @@ export function handleCliCommand(
   source: CliCommandSource = 'initial',
   deps: CliCommandServiceDeps,
 ): void {
+  if (args.logLevel) {
+    deps.setLogLevel?.(args.logLevel);
+  }
+
   const hasNonStartAction =
     args.stop ||
     args.toggle ||
diff --git a/src/main.ts b/src/main.ts
index 88419c0..4ed428e 100644
--- a/src/main.ts
+++ b/src/main.ts
@@ -1255,6 +1255,17 @@ function getResolvedConfig() {
   return configService.getConfig();
 }
 
+function getRuntimeBooleanOption(
+  id:
+    | 'subtitle.annotation.nPlusOne'
+    | 'subtitle.annotation.jlpt'
+    | 'subtitle.annotation.frequency',
+  fallback: boolean,
+): boolean {
+  const value = appState.runtimeOptionsManager?.getOptionValue(id);
+  return typeof value === 'boolean' ? value : fallback;
+}
+
 const {
   getResolvedJellyfinConfig,
   getJellyfinClientInfo,
@@ -2025,7 +2036,9 @@ const { reloadConfig: reloadConfigHandler, appReadyRuntimeRunner } = composeAppR
               appState.ankiIntegration.applyRuntimeConfigPatch(patch);
             }
           },
+          getSubtitleStyleConfig: () => configService.getConfig().subtitleStyle,
           onOptionsChanged: () => {
+            subtitleProcessingController.invalidateTokenizationCache();
             broadcastRuntimeOptionsChanged();
             refreshOverlayShortcuts();
           },
@@ -2296,13 +2309,21 @@ const {
       getKnownWordMatchMode: () =>
         appState.ankiIntegration?.getKnownWordMatchMode() ??
         getResolvedConfig().ankiConnect.nPlusOne.matchMode,
-      getNPlusOneEnabled: () => getResolvedConfig().ankiConnect.nPlusOne.highlightEnabled,
+      getNPlusOneEnabled: () =>
+        getRuntimeBooleanOption(
+          'subtitle.annotation.nPlusOne',
+          getResolvedConfig().ankiConnect.nPlusOne.highlightEnabled,
+        ),
       getMinSentenceWordsForNPlusOne: () =>
         getResolvedConfig().ankiConnect.nPlusOne.minSentenceWords,
       getJlptLevel: (text) => appState.jlptLevelLookup(text),
-      getJlptEnabled: () => getResolvedConfig().subtitleStyle.enableJlpt,
+      getJlptEnabled: () =>
+        getRuntimeBooleanOption('subtitle.annotation.jlpt', getResolvedConfig().subtitleStyle.enableJlpt),
       getFrequencyDictionaryEnabled: () =>
-        getResolvedConfig().subtitleStyle.frequencyDictionary.enabled,
+        getRuntimeBooleanOption(
+          'subtitle.annotation.frequency',
+          getResolvedConfig().subtitleStyle.frequencyDictionary.enabled,
+        ),
       getFrequencyDictionaryMatchMode: () =>
         getResolvedConfig().subtitleStyle.frequencyDictionary.matchMode,
       getFrequencyRank: (text) => appState.frequencyRankLookup(text),
@@ -2920,6 +2941,7 @@ const {
 });
 const createCliCommandContextHandler = createCliCommandContextFactory({
   appState,
+  setLogLevel: (level) => setLogLevel(level, 'cli'),
   texthookerService,
   getResolvedConfig: () => getResolvedConfig(),
   openExternal: (url: string) => shell.openExternal(url),
diff --git a/src/main/cli-runtime.ts b/src/main/cli-runtime.ts
index 21c2d17..5bf34d8 100644
--- a/src/main/cli-runtime.ts
+++ b/src/main/cli-runtime.ts
@@ -6,6 +6,7 @@ import {
 } from './dependencies';
 
 export interface CliCommandRuntimeServiceContext {
+  setLogLevel?: (level: NonNullable<CliArgs['logLevel']>) => void;
   getSocketPath: () => string;
   setSocketPath: (socketPath: string) => void;
   getClient: CliCommandRuntimeServiceDepsParams['mpv']['getClient'];
@@ -55,6 +56,7 @@ function createCliCommandDepsFromContext(
   context: CliCommandRuntimeServiceContext & CliCommandRuntimeServiceContextHandlers,
 ): CliCommandRuntimeServiceDepsParams {
   return {
+    setLogLevel: context.setLogLevel,
     mpv: {
       getSocketPath: context.getSocketPath,
       setSocketPath: context.setSocketPath,
diff --git a/src/main/dependencies.ts b/src/main/dependencies.ts
index 829fb2c..7260dbf 100644
--- a/src/main/dependencies.ts
+++ b/src/main/dependencies.ts
@@ -112,6 +112,7 @@ export interface AnkiJimakuIpcRuntimeServiceDepsParams {
 }
 
 export interface CliCommandRuntimeServiceDepsParams {
+  setLogLevel?: CliCommandDepsRuntimeOptions['setLogLevel'];
   mpv: {
     getSocketPath: CliCommandDepsRuntimeOptions['mpv']['getSocketPath'];
     setSocketPath: CliCommandDepsRuntimeOptions['mpv']['setSocketPath'];
@@ -254,6 +255,7 @@ export function createCliCommandRuntimeServiceDeps(
   params: CliCommandRuntimeServiceDepsParams,
 ): CliCommandDepsRuntimeOptions {
   return {
+    setLogLevel: params.setLogLevel,
     mpv: {
       getSocketPath: params.mpv.getSocketPath,
       setSocketPath: params.mpv.setSocketPath,
diff --git a/src/main/runtime/cli-command-context-deps.ts b/src/main/runtime/cli-command-context-deps.ts
index ebd31f4..5496d8c 100644
--- a/src/main/runtime/cli-command-context-deps.ts
+++ b/src/main/runtime/cli-command-context-deps.ts
@@ -2,6 +2,7 @@ import type { CliArgs } from '../../cli/args';
 import type { CliCommandContextFactoryDeps } from './cli-command-context';
 
 export function createBuildCliCommandContextDepsHandler(deps: {
+  setLogLevel?: (level: NonNullable<CliArgs['logLevel']>) => void;
   getSocketPath: () => string;
   setSocketPath: (socketPath: string) => void;
   getMpvClient: CliCommandContextFactoryDeps['getMpvClient'];
@@ -45,6 +46,7 @@ export function createBuildCliCommandContextDepsHandler(deps: {
   logError: (message: string, err: unknown) => void;
 }) {
   return (): CliCommandContextFactoryDeps => ({
+    setLogLevel: deps.setLogLevel,
     getSocketPath: deps.getSocketPath,
     setSocketPath: deps.setSocketPath,
     getMpvClient: deps.getMpvClient,
diff --git a/src/main/runtime/cli-command-context-main-deps.ts b/src/main/runtime/cli-command-context-main-deps.ts
index 831c89d..de46fa4 100644
--- a/src/main/runtime/cli-command-context-main-deps.ts
+++ b/src/main/runtime/cli-command-context-main-deps.ts
@@ -10,6 +10,7 @@ type CliCommandContextMainState = {
 
 export function createBuildCliCommandContextMainDepsHandler(deps: {
   appState: CliCommandContextMainState;
+  setLogLevel?: (level: NonNullable<CliArgs['logLevel']>) => void;
   texthookerService: CliCommandContextFactoryDeps['texthookerService'];
   getResolvedConfig: () => { texthooker?: { openBrowser?: boolean } };
   openExternal: (url: string) => Promise<unknown>;
@@ -51,6 +52,7 @@ export function createBuildCliCommandContextMainDepsHandler(deps: {
   logError: (message: string, err: unknown) => void;
 }) {
   return (): CliCommandContextFactoryDeps => ({
+    setLogLevel: deps.setLogLevel,
     getSocketPath: () => deps.appState.mpvSocketPath,
     setSocketPath: (socketPath: string) => {
       deps.appState.mpvSocketPath = socketPath;
diff --git a/src/main/runtime/cli-command-context.ts b/src/main/runtime/cli-command-context.ts
index d2aa185..5bba428 100644
--- a/src/main/runtime/cli-command-context.ts
+++ b/src/main/runtime/cli-command-context.ts
@@ -7,6 +7,7 @@ import type {
 type MpvClientLike = CliCommandRuntimeServiceContext['getClient'] extends () => infer T ? T : never;
 
 export type CliCommandContextFactoryDeps = {
+  setLogLevel?: (level: NonNullable<CliArgs['logLevel']>) => void;
   getSocketPath: () => string;
   setSocketPath: (socketPath: string) => void;
   getMpvClient: () => MpvClientLike;
@@ -54,6 +55,7 @@ export function createCliCommandContext(
   deps: CliCommandContextFactoryDeps,
 ): CliCommandRuntimeServiceContext & CliCommandRuntimeServiceContextHandlers {
   return {
+    setLogLevel: deps.setLogLevel,
     getSocketPath: deps.getSocketPath,
     setSocketPath: deps.setSocketPath,
     getClient: deps.getMpvClient,