RAID keeps rebuilding on boot

On boot, my system Raid1 (2 - 250gb WD HD - Intel Matrix 5) shows that it is degraded and rebuilds itself on booting into windows. Post time is painfully slow, HD stays on.
Intel Storage Matrix console says the RAID is rebuilding. After a long time, RAID rebuilds and computer works fine...HD light off and everything.

Then when I restart, RAID again degrades and rebuilds....

OK, I just had a really bad Virus, Trogan..and who knows what problem - it took me multiple passes and tries before I think I got it all....

Then this problem...

I want to think it is a registry problem, but don't know how to fix it.
Only other problem is program Icons lost many of their image associations - so I have to fix then one at a time - that must be a registry thing.

Any ideas, I'm going nuts with this stuff!!

Thank you in advance.

JP