There's no mystery of this sort that can't be solved, if you're willing to throw money at it, and feel having an answer would be worthwhile. The question is, does a problem that occurs for just a few moments after wake-from-sleep justify the expense? At this point, with the warranty expired, Apple has no obligation to spend the money, so it's up to you.
Clearly, system diagnostics found nothing, so Apple doesn't have a clear justification for replacing a particular part(s). Since, presumably, you'd be paying for the repair, give Apple credit for not asking you to spend money on replacing components on a guess, "We think it may be the main logic board. We can replace it to find out for sure."
There may be a hardware fault, but it could be very subtle. Since it only happens right after wake-from-sleep and self-corrects, it "feels" like hardware. If this was a CRT, nobody would give the issue a thought - CRTs are often unstable immediately after startup. Since LCDs don't have the same characteristics, a momentary instability is more noteworthy.
I'd connect an external display, and see if the issue is duplicated on the external - that could help narrow things a bit.
When you erased and reinstalled OS X, did you then immediately restore from a backup, or did you run the machine "clean" for a while, to test it?