Maybe a beginner problem

Methinks the "beginner problem" is that you even want to do that

first the 340 is not JTAG it is EC3.

I think Ii read above that "JATG disconnected" means the plug us pulled, if so I'll bet you have power supply problems.

I am not familiar with your specific chip, it differs quite a bit in the crossbar from the "common" but if SMB is separate from I²C the only 'real' diffrence between I²C and SMB is that SMB has a timeout.  would that be a possible solution.

PS why do you need two I²C ports?