Sounds to me like caching issues and maybe an indexing problem.
Type the following into terminal (or copy and paste):
sudo rm -rf ~/Library/Caches/* ~/Library/Application\ Saved\ State/* /Library/Caches/* /System/Library/Caches/* /private/var/folders/*
This will remove all caches from the system and then on reboot, the unit will rebuild them. Should help quite a bit.
Also, download Onyx (best program ever BTW). Under Automation, check off Repair Permissions,...