6i25 custom firmware and weird latency

Thanks, I'll check that also. Though the problem appears to occur no matter which GPIO I use for the PWM so it's probably not that. The PWM output also appears to work correctly.

I'll report back next week on my findings

Looks like it was a bad PC after all.

Trying the other PCIe slots on the motherboard, it crashed the whole PC immediately.
I measured the +12V and +3.3V voltages on the PCIe connector, but they both looked fine.
Probably some poor EMI-sensitive design on the motherboard.

Anyway, I got another PC and now it works fine with the same configurations.
Thanks for the troubleshooting help!

(For future reference, the bad PC was Fujitsu Esprimo E500 E85+)