X11 windows do not raise (come to the front) when the application is activated. This is a well-known bug in Tiger and the current X11 release. If you switch apps with the Dock, then you must click the X11 icon twice -- once to activate and once to bring the windows forward. If you switch apps (like I do) using Command-Tab, then you must Command-Tab to X11 a second time, e.g. with the key sequence Command-(Tab,Shift-Tab).
One workaround is to bind a new key to an AppleScript that activates X11. There are many ways to do this, but one way is to use Butler.
tell application "X11" to activate
Mac OS X Hints
http://hints.macworld.com/article.php?story=20050714011418999