Are there any other cards in there? Sounds kinda like the boot interrupt is being usurped by something (maybe with its own BIOS?) and never getting to the floppy / HDD. I assume you've set the boot order to A: or C:? I know, dumb question, just checking the obvious stuff.

The only other card is the video card.

When it tries to boot from the floppy, the LED actually does comes on, but the drive otherwise does nothing. Exactly the sort of symptoms you'd expect from a dead drive, but the drive definitely works perfectly... Even tried it with a Gotek USB thing and got the same symptoms.

What brand of IO controller is it? It doesn't happen to be a certain Kouwell KW-556N, does it? I have one of those that did the exact same thing in my 286 when I was building it a couple of weeks ago. It would say something like "Drive not ready" regardless of if there was a floppy in the driver or not. It didn't even check the drive. Rather odd.

I've tried a Goldstar Prime 2C and a UMC based one.

Tried using a BIOS from another random 386 board which made no difference. It POSTed and otherwise worked, but had the same issue.

hmm. If it were mine, I'd hook it up to the ol' HP 16500B logic analyzer to see what's going on with the floppy bus. I seriously doubt you have a 16500B, though. Do you have an oscilloscope, by chance?

Unfortunately not, I've had an oscilloscope on my shopping list for ages now but haven't gotten around to getting one.

Just did another check of the board to look for broken traces. Looks fine. Pretty much run out of ideas. I've tested all sorts of combinations of controllers/drives/cables. It's definitely the motherboard that's at fault.