Looks like this problem may have resurfaced. If you (i) modify a PIM, typically by tabbing around the PIM, and entering various index values, you'll notice that (ii) they are (typically) left justified within the PIM cell. Now..
1\ if you try to run the model with the modified, left-justified PIM open, MARK will not see/use the changed PIM index values. Instead it will simply use the default PIM index values.
2\ if you either (i) close the modified PIM before running the model, or (ii) use the '+' and -' buttons in the PIM to toggle up/down, which centers the new index values (or, open the PIM chart and move a few blue boxes back and forth, which amounts to the same thing), problem solved...
Gary is aware of the problem, and is working on a 'fix' that won't require you to remember step (2), above.
Stay tuned...