This is the second time in 5 years that I have accidentally encountered this issue, and I wanted to add a forum post to document its solution. When using PalletPro, don't try to get cute with the name of PLONPAL.TP if you want the simulation to work. There have been times when the path from infeed to build stations in a 2-cycle cell has been so different that I have decided to just create two different PLONPAL (example: PLONPAL1.TP, PLONPAL2.TP) programs rather than turn things into a branching mess. Both times I have done this, it has screwed up the roboguide simulation. Even though both copies of the PLONPALx.TP program contain the normal calls to TLK2PP,PMADDQ,PMDSPSPD,PMCHGPLD and whatever other supporting Karel programs are responsible for updating variables behind the scenes, something about changing the name does not jive with palletPro. Everything works fine running on the real robot, but the simulation does not update properly.
The issues caused by changing the name include cases not advancing down the infeed after each pick, Unit pres inputs/Ok2pick signals remaining on even with no cases at the in feeds, and units disappearing from the pallet after the place.
I'm not sure if similar issues happen when changing the name of default pallet tool programs.
Hopefully this helps somebody else (or me in another 5 years).