Yea, after hearing that your database is big I think that could also be a big problem. Have you converted it to PostgreSQL yet? If not, that is a must and will give you immediate results.

Also, for anybody who is into computers, has anybody used 2 Raptors in RAID to store their PT database on? I think that would have huge performance increases , but I want to make sure its noticeable before I shell out the money for it.