I've had similar problems. The problem was primarily with checking in imported geometry.
Installing the TS1093427 hotfix fixed the issue.
Make sure you do a proper backup and follow the instructions carefully.
I thinks that this error is coming from database itself. I tryed some maintenance scipts but nothing helped . The thing is that I can work normally for a few hours and suddenly everything is working very vey slowly and i get the error . Also when I am pointing on a folder inside the PS it takes 10 minutes maybe more to populate . I am thinking to do a reinstall of the entyre system .