This can occur on completely stock roms with no additional programs installed, and anything beyond. You can read on other users' experiences in these threads:
http://forum.ppcgeeks.com/showthread.php?t=29529
http://forum.ppcgeeks.com/showthread.php?t=22759
To sum it up, the issue will go away if you soft reset, or rotate to landscape mode, then back to portrait mode. Still no idea what causes it... hopefully HTC/Sprint will address it in the 6.1 release they're working on (note, the bug does exist in the Sprint 3.02 leaked rom).
Hope this helps.