Nate, if it's a design issue with the TV, there's nothing the repair
shop could do until and
if Sony fixes the problem and releases a replacement control board for it. The "repair" likely involved nothing more than a full checkout of the TV according to a factory test plan/specs, and replacement of anything questionable (especially since it was a warranty repair).
That said, if they found no problems with the electronics, they should have told you so that you'd know to look elsewhere for the problem.
How exactly are you using the TV? Do you have it hooked directly to cable (using the tuner) or using an external cable box? Does it flicker only when using broadcast/cable signals or when feeding it video?