I swapped out the replacement control board today and found that the same patch select encoder is even worse. This one can go several clicks with out responding, then go several clicks skipping a patch on EVERY click. What a wast of time. I'm going to have to take it all apart again, and put the original board back in and call it a day. I HATE encoders.
Sorry to read that. It's a bummer.

I'm an electronic hobbyist and after contacting DSI support and agreed on doing the encoder replacement myself (not the whole board, just the faulty encoder removal/replacement for which I have the necessary equipment and knowhow) I've received two new replacement encoders from DSI late last week, to swap the defective one with. But now that I've read your report, I'm hesitating to go ahead and perform the removal of 39 plastic knobs, 24 screws, to access it, desolder it, install the new one, solder it in place, and rescrewing 24 screws, putting back 39 plastic knobs, as shown on the link below provided by DSI, if the result could be possibly even worse:
https://www.davesmithinstruments.com/prophet-rev2-keyboard-right-panel-removal/ 
I think I'll wait for now, because the defective behavior is manageable. My defective encoder (Parameter) does skip a couple of values sometimes, and occasionally doesn't do anything for one step, but it still seems to work better than the ones on your replacement board.
I find it curious that DSI would have such (hidden) pages handy on their server (there is also one for the left panel removal), as if they were already expecting problems with some of their REV2s maybe ?
BTW, the 2 new encoders are really small and feel rather cheap, even compared to the one in my Behringer Deepmind 12 which is working flawlessly at any speed (and even has a smoother action).
I'm surprised that DSI didn't test the replacement board that they've sent you before shipping it...

I also really hate mechanical/electrical digital encoders

, unless they're optical like a computer mouse scroll wheel.