I have had my fair share of battles with "err 99". Tried all the fixes on the web I could find (pencil eraser the lens contacts, shut everything off & back on again) without lasting results. Finally I sent my 20D into Canon and $212 later was told there was a loose connection on the body's pcb (printed circuit board) that was causing the "err 99". Fine. Got it fixed.
Back in the groove and 5 freakin' frames into my son's kindergarten graduation-WHAM! "err 99". Got it home and tried my 70-200 f2.8L zoom...fired 30-40 frames without a problem. I began to realize that every time I experienced the "err 99" was with my EF 28-90 f4-5.6 starter lens.
Called Canon, sent the body and lens back. 2 weeks later, but with out additional charge, I got them back. Canon said the body was ok, but the lens AF was faulty, and repaired.
Back in the groove again, I'm happy so far...no problems.