I hear a bunch of extra off-key notes and some hanging, my first suspicion would be the HardMPU but others might have a better idea for you. I don't have experience with the MPU.

No idea on the HardMPU, if you have a sound card with a standard 15pin joystick port, I'd recommend just using that.
Also how are your cables connected? I think Doom is one of the games that does weird things if you have the SC-55's MIDI ouput connected to the computer's MIDI input. You should only use the computer output->module input part of your cable. You could also have a damaged MIDI cable, it happens more often then you'd think.

It's hard to say anything without knowing what your exact setup is, what cables you have, and what's connected, but I'd suggest trying a regular ol' sound card instead of the HardMPU and disconnecting the MIDI OUT on the SC-55. If that doesn't fix anything then maybe try new cables?

could be worth to do a reset on the sc-55 (or better yet just remove the internal cr-2032 battery) and try again

Thanks for the suggestions - as usual, I solved the problem on my own within hours of posting this thread.
I was using a Sound Blaster 32 PnP, and it was somehow conflicting with the HardMPU. I could not find a jumper on the board to disable the built in MPU emulation on the Sound Blaster, and I could not find a way to do it in the software either. So I replaced it with a Sound Blaster 16 that has a hardware jumper to disable the built in MPU emulation. I set that up, and it now works fine!

AppleDash wrote:

Sound Blaster 32 PnP . . . I could not find a jumper on the board to disable the built in MPU emulation on the Sound Blaster, and I could not find a way to do it in the software either.

You cannot disable the MPU-401 port on PnP Sound Blasters. But you can tell them to use different resources. Move the Sound Blaster's MPU-401 to an I/O port other than 0x330 and you should be all set.