overheating probs

ok, here is the setup:
AMD 2500+
MSI K7N2 Delta-L
80 WD 7200 HD
2 x 512 Kingston
ATi 9600 Pro
3 case fans, one exaust on side for video, one intake in front, one exaust in rear. Stock heatsink and fan.

i was fooling around and monitoring my temps during gameplay and noticed that my cpu was running a little warmer than usual, no biggie, like 48 drgrees Celcius. So i decided to take the case apart and clean it all out. After i did that i noticed it didnt make much of a difference so i decided to upgrade my Bios and see if that would make the temp read any different. Well i went to msi live update 3, updated my bios, and now my temps are in the high 50's!!!. So i took off my heatsink and cleaned the old thermal grease off of everthing and applied new thermal grease but to no avail. Now i get these little warning beeps from the MOBO everytime the temp gets into the high 50's. The program i am using to monitor my computer is the MSI PC Alert 4. The bios i was running was the original bios that the board shipped with.
should i not have updated???

constantly puzzeled,
Colin