JTAG Mk2 ICE & Studio4.10 debugging problems

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I'm using version 4.10 studio, and have a ATmega128 running code generated with the latest GCC using ext coff output. I am getting intermitttent problems with the JTAG mk2 ICE. I can't single step over a simple prinf statement (no interrupts), and often single stepping doesn't work. I occasionally get the disassembly window pop up, with a break point in the middle of a statment.

Interesting is I have an original JTAG MK 1 also, which works fine (albeit slower over serial) with the same code. So I don't think I have a problem with the code/compile/or ext coff.

I've tried the mk2 with serial, and at different jtag frequencies, same problem. I upgraded to the latest firmware. I tried using the elf passer also, same problem.

Anyone any idea what to try next.