Maybe the 3.12v is below the threshold voltage for the main CPU, but I'm just guessing. You could try contacting Roland for a schematic, or preferably the service manual. At the time it was manufactured there must have been some supporting documentation for their service centres.
Have you re-traced the steps you took when replacing the pot to make sure a connector isn't reversed or 1 pin out, or even if you have a solder bridge somewhere? All it needs is a tiny bead to bridge tracks and you've got a fault.
Before you replaced the pot did everything (apart from the pot) work correctly?