Thats the exact problem I was having without running Task29, partial Hard Resets in the middle of the night or after a couple hours of fresh flashes. Only the stuff that I had installed, all my cabs and customizations would delete themselves.
Task29 is VERY important.
I had a problem running Task29 from the .zip file so I couldnt do it till I found an all in one Task29.exe file that didnt require anything other than running it while synced with PC.
You can find it here:
http://www.ziggy471.com/downloads/Task29.exe