Windows 7: Annoying lags

So I was under Windows Vista. Some weird problems were already happening: lags causing the system to freeze, or it would crash directly too. That was making it reboot. But it wasn't happening so often. Note I still had to repair Windows with the DVD when it happened. And it wasn't a virus: I had Avast! running all the time, and up to date.

Now, I switched to Windows 7. Clean installation, formatted my main HDD before installing Windows on it. Thought it was going to get me rid of the weird things described above: wrong. Quite often, one application (mostly Firefox/IE), or the desktop/taskbar stops responding for no reason. No abnormal CPU/memory usage or big HDD access registered during those lags. Sometimes it will make other applications lag. Can get so bad that the system reboots the computer. It happens rarely enough, but when it happens, in the best case, I have to wait for it do perform a checkdisk; in the worst case, I have to take my Windows 7 DVD and repair the OS, otherwise it'll just stay forever on the bootscreen, or reboot again and again. Each time the repairing process ended, I looked at the log: each time it said the filesystem was damaged. What the hell would have damaged it?

That's Really Annoying. I really hope someone can help me to find a solution for those problems.

And, last precisions, I have installed Avast! on my fresh Windows 7 and it's up to date. So I don't think it's a virus. I suspected it could be a hardware problem; checked, my motherboard does have the latest BIOS. But, upon boot, it first says "detect drives done, no any drive found", then reboots, and the second time drives are correctly detected and Windows boots normally.