Hello Doug,
It would seem unusual to have a STOP instruction within ISR code. Conventionally, I would assume that all pending tasks, as a result of hardware interrupts, would usually need to be completed before entering one of the STOP modes. However, I can't see a reason why the instruction should not work within the ISR, particularly for STOP1.
It is not clear to me whether you are using full chip simulation, or are debugging the actual device using BDM. If using simulation, it would not surprise me if there were problems in simulating stop mode.
However, for debug using BDM, I wonder if STOP1 is actually entered whilst BDM is enabled. Does the problem persist with BDM cable disconnected?
Regards,
Mac