I (USC) cross the border on foot. The Turkish side stamps, the EU side didn't. It was clear that the EU side couldn't give a hoot about the lack of entry/exit stamps into Greek Cypirot territory.
In brief, don't fret.
p.s. if you're worried about not having the EU entry stamp and eventually exiting through the EU, too, don't. I've had the same issue with landing at FCO and leaving from MUC (Italy...doesn't always stamp).