diff --git a/src/custom-stdio.ts b/src/custom-stdio.ts
index 4c868c90..e1c3bb4c 100644
--- a/src/custom-stdio.ts
+++ b/src/custom-stdio.ts
@@ -277,6 +277,7 @@ export class FilteredStdioServerTransport extends StdioServerTransport {
 
   /**
    * Public method to send log notifications from anywhere in the application
+   * Now properly buffers messages before MCP initialization to avoid breaking stdio protocol
    */
   public sendLog(level: "emergency" | "alert" | "critical" | "error" | "warning" | "notice" | "info" | "debug", message: string, data?: any) {
     // Skip if notifications are disabled (e.g., for Cline)
@@ -284,6 +285,17 @@ export class FilteredStdioServerTransport extends StdioServerTransport {
       return;
     }
     
+    // Buffer messages before initialization to avoid breaking MCP protocol
+    // MCP requires client to send first message - server cannot write to stdout before that
+    if (!this.isInitialized) {
+      this.messageBuffer.push({
+        level,
+        args: [data ? { message, ...data } : message],
+        timestamp: Date.now()
+      });
+      return;
+    }
+    
     try {
       const notification: LogNotification = {
         jsonrpc: "2.0",
@@ -315,6 +327,11 @@ export class FilteredStdioServerTransport extends StdioServerTransport {
    * Send a progress notification (useful for long-running operations)
    */
   public sendProgress(token: string, value: number, total?: number) {
+    // Don't send progress before initialization - would break MCP protocol
+    if (!this.isInitialized) {
+      return;
+    }
+    
     try {
       const notification = {
         jsonrpc: "2.0" as const,
@@ -346,6 +363,11 @@ export class FilteredStdioServerTransport extends StdioServerTransport {
    * Send a custom notification with any method name
    */
   public sendCustomNotification(method: string, params: any) {
+    // Don't send custom notifications before initialization - would break MCP protocol
+    if (!this.isInitialized) {
+      return;
+    }
+    
     try {
       const notification = {
         jsonrpc: "2.0" as const,
diff --git a/src/index.ts b/src/index.ts
index ef179f87..450d895c 100644
--- a/src/index.ts
+++ b/src/index.ts
@@ -39,6 +39,13 @@ async function runServer() {
     // Set global flag for onboarding control
     (global as any).disableOnboarding = DISABLE_ONBOARDING;
 
+    // Create transport FIRST so all logging gets properly buffered
+    // This must happen before any code that might use logger.*
+    const transport = new FilteredStdioServerTransport();
+    
+    // Export transport for use throughout the application
+    global.mcpTransport = transport;
+
       try {
           deferLog('info', 'Loading configuration...');
           await configManager.loadConfig();
@@ -56,10 +63,6 @@ async function runServer() {
           // Continue anyway - we'll use an in-memory config
       }
 
-    const transport = new FilteredStdioServerTransport();
-    
-    // Export transport for use throughout the application
-    global.mcpTransport = transport;
     // Handle uncaught exceptions
     process.on('uncaughtException', async (error) => {
       const errorMessage = error instanceof Error ? error.message : String(error);
diff --git a/src/utils/feature-flags.ts b/src/utils/feature-flags.ts
index be78145a..2c711623 100644
--- a/src/utils/feature-flags.ts
+++ b/src/utils/feature-flags.ts
@@ -46,6 +46,10 @@ class FeatureFlagManager {
         });
       }, this.cacheMaxAge);
       
+      // Allow process to exit even if interval is pending
+      // This is critical for proper cleanup when MCP client disconnects
+      this.refreshInterval.unref();
+      
       logger.info(`Feature flags initialized (refresh every ${this.cacheMaxAge / 1000}s)`);
     } catch (error) {
       logger.warning('Failed to initialize feature flags:', error);
@@ -107,7 +111,7 @@ class FeatureFlagManager {
    */
   private async fetchFlags(): Promise<void> {
     try {
-      logger.debug('Fetching feature flags from:', this.flagUrl);
+      // Don't log here - runs async and can interfere with MCP clients
       
       const controller = new AbortController();
       const timeout = setTimeout(() => controller.abort(), 5000);
@@ -132,10 +136,9 @@ class FeatureFlagManager {
         this.flags = config.flags;
         this.lastFetch = Date.now();
         
-        // Save to cache
+        // Save to cache (silently - don't log during async operations
+        // as it can interfere with MCP clients that close quickly)
         await this.saveToCache(config);
-        
-        logger.info(`Feature flags updated: ${Object.keys(this.flags).length} flags`);
       }
     } catch (error: any) {
       logger.debug('Failed to fetch feature flags:', error.message);
@@ -154,7 +157,7 @@ class FeatureFlagManager {
       }
       
       await fs.writeFile(this.cachePath, JSON.stringify(config, null, 2), 'utf8');
-      logger.debug('Saved feature flags to cache');
+      // Don't log here - this runs async and can cause issues with MCP clients
     } catch (error) {
       logger.warning('Failed to save feature flags to cache:', error);
     }