diff --git a/src/services/worker/ProcessRegistry.ts b/src/services/worker/ProcessRegistry.ts
index cd7dab89..e4888d26 100644
--- a/src/services/worker/ProcessRegistry.ts
+++ b/src/services/worker/ProcessRegistry.ts
@@ -416,7 +416,23 @@ export function createPidCapturingSpawn(sessionDbId: number) {
     // causing subsequent flags to be consumed as values for the preceding flag.
     // The Agent SDK may produce empty-string args (e.g., settingSources defaults to []
     // which joins to ""). Node preserves these, but Bun drops them, breaking CLI parsing.
-    const args = spawnOptions.args.filter(arg => arg !== '');
+    //
+    // FIX: Simply filtering empty strings has the same effect as Bun dropping them —
+    // it leaves the preceding flag (e.g. --setting-sources) without a value, causing
+    // the next flag (e.g. --permission-mode) to be consumed as that value.
+    // Instead, we must remove the entire flag+empty-value pair.
+    const args: string[] = [];
+    for (let i = 0; i < spawnOptions.args.length; i++) {
+      const arg = spawnOptions.args[i];
+      if (arg === '') continue; // skip standalone empty strings
+      // If this is a --flag followed by an empty string, skip both (remove the pair entirely)
+      if (arg.startsWith('--') && i + 1 < spawnOptions.args.length && spawnOptions.args[i + 1] === '') {
+        i++; // skip the empty value too
+        continue;
+      }
+      args.push(arg);
+    }
+
 
     const child = useCmdWrapper
       ? spawn('cmd.exe', ['/d', '/c', spawnOptions.command, ...args], {