I found out that it is indeed OK to have different thicknesses of pallet to ensure that the drop is the same on both pallets.
I made up a sliver of gauge plate, filed to size, hardened, soldered to pallet and ground to shape. Not an easy job, but it has fixed the problem.
The pallets are now operating correctly, and the clock is ticking away as it should.
This was a tricky one for me to diagnose and get the geometry right but all the more satisfying now that it is working.