Serbia doesn't recognize the existence of Kosovo: they consider it a province of Serbia. That being the case, if you enter Kosovo from anyplace but Serbia, that means you've entered Serbia itself. If you don't have a Serbian entry stamp--which you don't because Kosovo is actually NOT a province of Serbia--you're in the country illegally.
The solution is to enter Kosovo from Serbia. You can then exit back into Serbia, since they believe you haven't left the country at all. Simple. Or you can enter and exit without going through Serbia at all; they're ok with that. You can then enter Serbia by any other border without problems.
I'd be surprised if there are days or border stations where this is not an issue; it's a matter of deeply-wounded national pride to Serbians, and Serbians are very good at taking insult and feeling aggrieved for, say, a couple of centuries or more.
Mark
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