New motherboard, slower PC

Hi all. I'm not sure if that's the right section for my problem, so if it's not then I'm sorry.

A few days ago I've replaced my motherboard, since the the AGP port on the other one got broken. I bought MSI RS350M-ILSR (MS-7031) motherboard (info from Everest). The problem is, everything is WAY slower than before. Games that ran perfectly are now a slideshow, like World in Conflict, or HL2 for example. Hell, even quake 3 runs way worse than before, sometimes dropping under 90 fps even tho it was 125 all the time before. I thought it may be the driver issue since it's a different motherboard, so I reformatted C drive and did a clean windows install. That didn't help. Even the installation took way longer than before, let alone the formatting. I tried using an onboard vid card, but that didn't help, neither did using a better PSU. Of course I installed the drivers I could find for my motherboard and vid card. The temps. are the same as they were on the previous motherboard. I couldn't find the info on the motherboard anywhere for some reason, but I can upload the PDF manual if anyone wants. My configuration:
Intel Pentium 4 Prescott 3.2ghz (LGA 478)
Radeon x1650 512mb (AGPx8)
1024 ram
MSI RS350M-ILSR (MS-7031) Motherboard
320gb Seagate SATA drive
Modecom Feel 400w PSU (Also checked it on 550w Chieftec and it didn't help)
Please help. Thanks in advance.

What operating system are you running? Have you applied the latest drivers for your "new" motherboard AND the Radeon AGP video card?

I'm running Windows XP Proffesional. Yes I installed drivers for motherboard and Vid card.

often with old games like quake and HL they don't function properly with the new drivers

The point is that EVERYTHING was working like 2 times faster than it does now. Formatting, defragmenting, games, installing Windows, et cetera...