Ok, this is a strange one.
By any chance has someone noticed any issues when using a Hori Fighting commander on any PCE hardware.
I recently picked up the HFC pad and tried it on my LT and noticed that I got strange button responses - like for some reason in SFII sometimes a punch would result in a kick or more noticeably when i jumped over to the P2 side I found that when I tried to do a dragon punch it paused the game or it never registered the punch button at all.
The weirdest thing that happened though was that I managed to get a 2 player game going somehow (no multi-tap was connected) and was able to control both players with the pad (and the LT controls).
I actually have a video of the latter;
Anyway, tests I did after this;
1) Plugged in a Avenue 6B pad - worked fine.
2) Used the HFC on my Duo - worked fine.
3) Tried the HFC with the Everdrive - had the same issue.
So it would seem that there is definitely an issue between the HFC and the LT.
Just thinking out loud here, maybe some earlier hardware configs weren't 100% compatible with all third party peripherals? I didn't get round to testing a regular Core Grafx yet and perhaps that might show something as the hardware is similar to the LT.
The only other way to test it would be to try another HFC.