When you manually set it to what the default settings are anyway, there's no actual change made to the system. The BIOS is probably just sensing that it's not in "auto mode" or whatever. I wouldn't worry about it. Verify that your voltages and CPU temperatures are where they're supposed to be though.
Can you describe the slow-downs that occur when you use Auto settings? Are you referring to the Cool 'n Quiet feature that lowers the CPU speed when you don't need the CPU to be running at 3.0GHz?
Phenom II X4 925c2 @ 2.80GHz (95W)
OCZ Platinum PC3-1333 2x2GB 7-7-7-21
Raidmax RX-500AFCheck it out.