I'm not sure if it can be updated via jtag but in anycase after emailing Marshall he was able to help me fix the problem via some new firmware update betas he's apparently been working on those of course being known as the 1.05 betas.
I tested both at Marshall's urging and the first one solved 99% of the problems the 1.04 update was causing me and the second version of the 1.05 update that he gave to me solved my console's problems as far as I can tell 100%.
Hopefully for everyone else's sake my console was the only one having issues on the 1.04 firmware as I believe Marshall's latest batch of boards that have just recently gone out may all be operating on the 1.04 firmware.