SuperNt has a bit of a strange booting behaviour, it seems that a change in CIC state / pair mode entry can make it crash.
The SuperCIC firmware on the OG sd2snes technically had a bug which always makes the CIC handshake fail when resetting the console after entering pair mode. SuperNt behaves differently from a usual SNES in that it resets the CIC twice on bootup instead of only once. Therefore it has some come to rely on pair mode entry never working properly. So the SuperNt tends to crash when SuperCIC handshakes actually work properly as is now the case with sd2snes / FXPAK pro!
By the time I noticed the difference it was too late

So I implemented a workaround that momentarily delays pair mode entry on console reset... it appears that it isn't working for everyone so this needs more attention. I suspect that there are also differences in behaviour depending on the model of the SuperNt (different SuperCIC lock firmwares used...?)
Either way this problem should only occur when pair mode is allowed in the FXPAK configuration.
To check if pair mode is allowed, open sd2snes/config.yml on your SD card and look for the option "PairModeAllowed". Setting it to 'false' might help with the issue at hand.
On a side note, CIC clock is super low on SuperNt. Usually it's between 3 and 4 MHz depending on the SNES model. SuperNt runs it at ~1.7MHz. But that shouldn't matter in normal operation.
As for the diagnostic firmware failing, that's most likely due to the SuperNt not booting up in time for the test. Results may also change when setting it to boot directly to the cartridge without entering the splash screen or the menu.