[OMGWTF_BBQ]

I too have been having this same issue with my Stock Sprint 6.5 ROM.
I currently have Co0kie's home tab installed but even before I added it I had this problem. It hasn't occured in while, which is actually quite strange. I had another issue that I saw someone address in another thread about extreme lag and system crashes when exiting the default Windows Mobile text threads and going back to the messaging home screen. Again, I also had this problem. What I ended up doing is deleteing all (2000+) of my saved text messages and both problems seemed to dissapear overnight.
When I first upgraded from 6.1 to 6.5 I was furious but after tweaking it here and there it seems to work much better. Another suggestion I have is to disable animations on the home screen. Both animated wallpaper and weather. That seemed to speed everything up. Also HTC task manger, as much as I LOVE it, it killed my Touch Pro 2. I highly recommend uninstalling it if you have added it.
Last but no least, anyone having the problem with the HTC Sense MP3 player pausing during play back? Because if so I have a solution.