Have you tried dumping your Preferences folder?
It sounds a little silly, but when a problem resurfaces between complete system wipes and re-installs, and the problem resurfaces after the user account is restored, a corrupted preference file tends to be the culprit.
There's a few easy ways to test this, most of which involve logging in from another user account. I would follow these steps…
1. Create a new user account with admin privileges (name it `Debug` or something)
2. log in under that account
3. open a Finder window, click `Go` in the menu, hold the `option` key, and click `Library`
4. move the `Preferences` folder to your desktop
5. reboot and log into the normal account
You will find that all your OS settings — and all non-sandboxed app settings — have been reset to new/factory conditions. This isn't as much trouble to sort out as it sounds like.
Use the account for a few hours or a day or two. If everything seems fine, just delete the `Debug` account and kiss your old Preferences goodbye.
If the problem resumes, this whole diagnosis was wrong, so you might as well log back into `Debug` and put your Preferences back.
(Don't worry about sandboxed prefs, that's all third-party and it's difficult to imagine a circumstance where that could be causing this… it has to be some system level thing)