I have been building retro pcs only for couple of years. I have had a strange problem with 386 and 486 motherboards. I think about half of the all the motherboards I have, have bit similar problem. Everything else works, but only thing that doesn't work is a floppy drive connected to the system.
I know the reason is the motherboard because everything else has been switched around and problem still stays with each of the motherboards. There are minor differences in what way the floppy drives don't work with the motherboards. Some don't recognize that there is floppy disk in the drive and give error that drive is not ready, some show that there is a floppy disk inside the drive but dir command shows like all the floppy drive is empty and some motherboards show that the directory listing is just random character. Hard drives work fine with each of the motherboards and it doesn't matter if it is on board ide or separate isa controller.

I am just curious if problems like these are really that common that floppy drive problems are the first thing that shows that something is wrong with a motherboard. Also I would like to know if anyone has ever managed to fix such problems.
I think my latest 486 board is my 4th or 5th motherboard in last 2 years with this kind of problem.