Pretty hairy story. There is nothing *normal* that would cause the XP to say a disk is unformatted if it in fact has been formatted, so it's either a faulty disk drive or a faulty disk. The latter is easier to determine than the former.
I would definitely mark the disks (was it one or two?) that prompted the synth to give the unformatted message, and put them aside. Start out with new diskettes and see if it happens again. If it does, evidence is mounting that something is wrong with your drive. If it does not, it was probably the disks themselves. You can always get the drive replaced and buy new diskettes.
Also, be careful when copying between disks: The backup function won't work between HD and DD disks.
Other than that, I think you're in the familiar world of determining by the process of elimination whether it's the drive or the diskettes. After starting out with new diskettes, if the problem doesn't recur, I'd probably dump the disks that originally prompted the problem.
Good luck.