Thank you for this information. It wasn't quite that simple; I needed to install the full 3.6.2, which was painful, but that fixed it.
I first added the reg_ptr->INTC.WCR = 0x80; line, but the INTC struct wasn't defined in mcf51JM.h. So I tried updating that file, but it still wasn't working. I installed 3.6.2 and rebuilt the new bsp and psp projects, then the application project, but that was worse (the debugger kept stalling in _int_kernel_isr in dispatch.s). So I created a new MQX project and imported the source files and finally I got it all to work as expected.
I'm not sure if this is normal (that I can't rebuild a project started with an older version of MQX after upgrading).
I also noticed that the bsp shows several files that are missing from the original (3.6.0) locations including maximum_config.h, small_ram_config.h, smallest_config.h, etc. In the 3.6.0 directory structure they appeared in ...\mqx\build folder, but they are not in the new structure (as reported by CW). They do still appear in the lib folders for the respective platforms. Is this normal that these files are included in the bsp project but aren't actually there? Should I just remove them or do I need to do something else?
Thanks again for your help.