Not sure if anyone else had this problem with the Rhodium Programs tab, it would link to the Start menu sometimes causing loss of TF3D menu scroll and soft keys. Found the fix for this over at XDA thanks to Showaco. Make sure you use v4.1, both 3 and 4 icon column work perfectly depending on your preference.
http://forum.xda-developers.com/showthread.php?t=487192
Edit: Found a better fix for this attached below. Might need both not sure though.