JTAG problems with Linux PC

I have an odd problem with my Linux PC. I can build and debug projects for my Cyclone development board (Cyclone 1c20) but I cannot debug my target hardware (Cyclone 1c12) under Linux even though the Windows IDE works fine. The code downloads ok but the sysid never matches and returns odd timestamps and IDs. The JTAG connection itself seems ok because nios2-terminal receives all the printfs.

Since I don't have a Quartus license for Linux I run SOPC/Quartus under Windows and then run NIOS IDE under Linux so I generate my system libraries based on a PTF file that I copy from the Windows to the Linux machine. Again, this works great for dev board projects but not for my target board.

Any ideas what I should try?

Thanks,

Andrew