Have you made any adjustments in the radio communications parameters? The defaults are CAT BPS 4800N82, CAT TOT 10msec.
I would take a look at the N1MM settings, and the FT5000 settings, to make sure all the settings agree. I would also try changing the baud rate, and making the CAT TOT a different number. It could be, when tuning the radio, it isn't updating in time to make the correct radio data for the computer. You may have to juggle baud rates and polling times to find something that will work with your new setup. What works with this setup may also be different that what will work with another setup.
I would also update N1MM Logger to version 14.3.1 or better. In the version 13.9.1, there was a bug where the semi-colon key would stop emulating the INS key, and the single quote key would stop emulating the "TU OH6LI" message.
By the way, I was part of the SE0X M2 as a remote operator- I was the op that worked you on 20M while sitting in my house in Marlborough, Ma, USA!
Dennis W1UE