TinkerTool System Release 2 (Legacy version) has been touted as offering the deepest cache clearing functionality; I've got no idea if it's your answer, but it's worth a try.

I'd also try booting into Safe Mode to see if there's anything to be learned: What is Safe Boot, Safe Mode?

Edit: Did you install any new apps immediately before your issue reared its ugly head?

Last edited by artie505; 01/07/15 07:46 AM.
The new Great Equalizer is the SEND button.

In Memory of Harv: Those who can make you believe absurdities can make you commit atrocities. ~Voltaire