MBPr losing gestures 2-3 times per day?

I trying to figure out if this is a hardware issue or software issue. When waking up my MBPr, about 2-3 times per day it will have lost OS gestures (not Safari gestures). This is fixable by killing the Dock process, but that's ridiculous to have to do multiple times per day. Has anyone else noticed this? I'v tried resetting the PRAM and NVRAM with no success. I talked to someone at the Genius bar who said they can't do anything about it but replace the whole unit (new unit came in, has horrible screen bleed, I'm sending it back and keeping my current one until then). He thought it may be a fault trackpad cable, but I would think the issue would be more consistent if that were the case.

Thoughts? I would just reinstall the OS, but I figure restoring from Time Machine will just bring back any software problems.

I'm still new to Time Machine. If I do an OS restore, will restoring from Time Machine just reintroduce problems? Or can specific folders be restored, like my music folder, development libraries, pictures, ect?

I think I'v found the culprit. After more searching, it seems that non Apple screensavers are messing with Mission Control, which messes up gestures. I has an older version of the widely used Clock screensaver seen here on Macrumors. After disabling it, the issue seems to be resolved. Hopefully 10.8.2 will bring a fix for this.