diff --git a/config/nginx_project.conf.template b/config/nginx_project.conf.template
index c89de7f..cba91ef 100644
--- a/config/nginx_project.conf.template
+++ b/config/nginx_project.conf.template
@@ -11,12 +11,15 @@ location ^~ /{{HOST}}/ {
         fastcgi_pass 127.0.0.1:{{PHP_PORT}};
         fastcgi_index index.php;
         
-        # Correctly use $request_filename for alias compatibility
-        include "{{CONF_DIR}}/fastcgi_params";
-        fastcgi_param SCRIPT_FILENAME $request_filename;
-        fastcgi_param DOCUMENT_ROOT $document_root;
+        # Split path info to handle subdirectories correctly
+        fastcgi_split_path_info ^/{{HOST}}(.+\.php)(.*)$;
         
-        # Optional parameters for frameworks
+        include "{{CONF_DIR}}/fastcgi_params";
+        
+        # Bulletproof SCRIPT_FILENAME: combine base path with relative script name from split_path_info
+        # On Windows + Alias, $request_filename can be flaky during try_files redirects
+        fastcgi_param SCRIPT_FILENAME "{{PATH}}$fastcgi_script_name";
+        fastcgi_param DOCUMENT_ROOT "{{PATH}}";
         fastcgi_param PATH_INFO $fastcgi_path_info;
     }
 }
diff --git a/src/main/ipc/index.ts b/src/main/ipc/index.ts
index db1dfc3..9a756fd 100644
--- a/src/main/ipc/index.ts
+++ b/src/main/ipc/index.ts
@@ -56,12 +56,26 @@ async function rebuildNginxConfig(forceProjects: boolean = false): Promise<{ bin
     const projects = await projectService.getProjects()
     for (const p of projects) {
         const projectConfPath = path.join(projectsConfDir, `${p.host}.conf`)
-        if (forceProjects || !fs.existsSync(projectConfPath)) {
+        let shouldGenerate = forceProjects || !fs.existsSync(projectConfPath)
+
+        // If file exists, check if it was manually edited
+        if (!shouldGenerate && fs.existsSync(projectConfPath)) {
+            const currentContent = fs.readFileSync(projectConfPath, 'utf8')
+            if (currentContent.includes('# MANUAL_EDIT')) {
+                shouldGenerate = false // Never overwrite manual edits during auto-rebuild
+            } else if (forceProjects) {
+                shouldGenerate = true
+            }
+        }
+
+        if (shouldGenerate) {
             const phpPort = portMappingService.getPhpPort(p.phpVersion)
             const normalizedPath = p.path.replace(/\\/g, '/')
+            // Ensure path ends with a slash for alias compatibility
+            const pathWithSlash = normalizedPath.endsWith('/') ? normalizedPath : `${normalizedPath}/`
             await configService.generateConfig('nginx_project.conf.template', `projects/${p.host}.conf`, {
                 HOST: p.host,
-                PATH: normalizedPath,
+                PATH: pathWithSlash,
                 PHP_PORT: phpPort.toString(),
                 CONF_DIR: confDir.replace(/\\/g, '/')
             })
@@ -510,8 +524,12 @@ export function registerIpcHandlers(): void {
 
     ipcMain.handle('project:nginx:save', async (_event, host, content) => {
         const configPath = path.join(configService.getBasePath(), 'generated_configs', 'projects', `${host}.conf`)
-        fs.writeFileSync(configPath, content)
-        // Full restart after manual project save
+        // Ensure manual edit marker is present
+        let finalContent = content
+        if (!finalContent.includes('# MANUAL_EDIT')) {
+            finalContent = `# MANUAL_EDIT\n${finalContent}`
+        }
+        fs.writeFileSync(configPath, finalContent)
         return await restartNginx()
     })