I bought a finished padhack (2xPSX pads + JAMMA fingerboard) from a random forum dude so I don't know what controllers were used. But I never had any issues using my J-Pac either. I've never tried Daytona though, as I only play shmups on my DC.
Maybe if you use your original DC controller without a Memory card inserted with Daytona to troubleshoot you'll get closer to a solution? The port might have an autosave option acting funny?