Is the new governor encoder the same rpm rating?
What does the Debug Screen show under Motion Excuses while the unit is faulted?
Dragging/sluggish brake (already mentioned) will cause a 27.
Flakey brake switch (if used) will generate a 27/26 fault.
Bad contacts, broken wires at Brake relays (SB, SB2 I think).

Faulty Brake Pick issues typically appear in Motion Region 2 or 3.