Repetier firmware has a rotary encoder speed setting, which I believe is there for software button de-bouncing. I think that I remember you posting that you switched to Marlin recently, and I don't know if it has an equivalent setting option. If you want to rule out the firmware, you could use the Repetier firmware web configuration program to slap together a quick firmware just to test the display hardware and encoder. Try all three rotary encoder speed settings to see if any of them fix the problem.....
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