I just got my new UC3B0256 PCB design, and I'm testing it now.
In my design, I also used TDI,TDO and TMS as GPIO pins and they are connected to a level translator IOs, and the level translator can be disabled (when the level translator IO become high-Z) by another GPIO.
I got some strange comunication stability problem for my JTAGmkII interface. A lot of times after I downloaded the program and unplug the JTAG connection, and program works, and after some time connect it back again and try to talk to it in AVR32studio and then there is no connection and it just give me a lot of JTAG errors. It seems the PCB always needs to be completely unpowered for a little while before the JTAG communication works again.
I'm sure that my JTAG interface logical connection is correct. But just wondering what happens when the program I downloaded is using TDI,TDO and TMS, and AVR32studio starts to talk through JTAG? Will it always reset UC3B first and then try to enter the JTAG mode?