I had been using my JTAGICE Mk II with the STK526 (which has an AT90USB162 @ 8MHz on it) for development, and everything has worked fine. Then I switched to my own design where the '162 runs at 16MHz. Now I find that when I attempt to debug, the '162 is not fully programmed -- one or two blocks of 128 bytes are 0xFF instead of program code. The position of these unprogrammed blocks seems to be random and changes each time.
I get the same results on AVR Studio 4.13 SP1 and SP2. The AVR Dragon works fine (allowing my work to continue). The JTAGICE will program the '162 fine with ISP.
I tried setting the JTAGICE options to not reprogram the device when entering debug mode, after programming it successfully with ISP. However, instead of leaving the program intact the device was erased!
I'm thinking this is a problem with the JTAGICE firmware, but I would appreciate hearing if anyone else has any other insights, or has been able to make this work.