Make sure you are not in MSDOS compatability mode or something strange like that ( I think this only affects hared drives ). Maybe Windows configured the drive wrong or recognized it as something else. Or maybe it is checked with disable in this profile or something like that. The Icon should say floppy, not removable disk media or anything strange.
I've never seen it, but I wonder if it could be a simple IRQ conflict. It could be configured properly, but some other hardware could be trying to use the same irq. I dont even know if this is a possibility.
I know my BIOS didnt want to configure my floppy correctly. There were options for different kinds of floppy drives, as well as what drive to boot from first. It is possible to select to boot from the A drive and then have NONE selected for the type of floppy on the BIOS. If you do not like my post feel free to point out your opinion or my errors.