Is there an option to disable ACPI in BIOS and revert to APM?
I don't know if this will help with the ISA issues but ACPI is hard-wired to IRQ9 so maybe there is some resource conflict going on there.
On my 233mmx system I had to revert to APM several years back when Phil discovered that ACPI IRQ9 messed up with his PCI SATA controller in a SS7 system. I had a similar setup (no sata but mpu401at installed so I needed IRQ9) and after testing with Gateway I really found out there was a conflict that was not apparent in other games. Reverting to APM solved this for me so from that point onwards I use APM.
I have no real experience though with ISA cards and anything faster than a 233mmx system... but could worth to try what I suggest.

Hi, Keropi!

I'm actually using your MPU card 😀 I don't think anything uses IRQ9 right now: MPU is set to default 330/IRQ2, and SB16 to 300/IRQ5, but I'll check it tonight. I think I've had ACPI issues on a Super Socket 7 motherboard before, so it feels like a good guess.

^ yep I figured it was PCMIDI 😀
acpi is weird in it's irq9 hogging - I was using my 233mmx setup for years but I did not realize I had an issue - Phil found it sooner since it was affecting his HDD
I hope there is an option for ACPI in your system, at some point they removed the ability to disable it fully - there are reports that even when BIOS has it to DISABLED it does not really free IRQ9

Aren't IRQ2 and IRQ9 the same thing? Believe the 16-bit IRQ controller is cascaded to the 8-bit one on IRQ2.

Sooo, the motherboard used APM, not ACPI.

I ended up reinstalling Windows after cleaning BIOS settings. Oddly enough, everything just works now, without any BIOS tweaks. I did have to manually specify IRQ and DMA for SB16 in the Device Manager, but I can freely switch between MT-32 and SC-55 now, I get proper SB16 sound and generally have no issues. My theory is that the BIOS update could have helped. Otherwise I have no idea what I did differently this time.

Still I'm curious why Permedia doesn't work with BIOS.

Scratch that, SB16’s MPU still doesn’t work. So MT-32 via MusicQuest works just fine, but SC-55 gives me weird issues.

1) Doom feels like 5 FPS even in start menu and takes long to launch. No sound or music
2) Duke Nukem 3D lags at launch but starts with both sound and music. It lags at the very beginning but then the FPS becomes okay. It does skip a few MIDI notes here and there.
3) somehow this time Device Manager shows that I have three MPU 401 devices
4) ACPI isn’t on. APM is, however.
5) no IRQ or DMA conflicts. I’ve set all the resources for SB16 and MusicQuest manually. No conflicts in Device Manager or AIDA32

Update. It all works!

First of all, my mistake was that I plugged both IN and OUT cables into SC-55. This is why Doom didn’t work.

Second, Duke Nukem simply is buggy with the MPU401 on CT2230.

So, apart from the BIOS update and manual resource assignment in Windows Device Manager I didn’t really have to anything to get things working.

I also realised that my MusicQuest card has two OUT ports. So I can just get a second MIDI cable and connect both Roland modules to the controller. That will solve my bugs in Duke Nukem 3D.