Well, I can tell you that your using NTFS has NOTHING to do with the problem you're having, which is probably of little to no comfort.
Given that it sounds like you did a new install, are you sure your system is free of viruses and spyware? Have you installed all the latest updates available? Are you certain that the floppy drive hasn't given out?
Just some basic things to try before moving on to other possibilities.
I have recently reformatted my C: drive from FAT to NTFS; now my floppy drive doesn't work. Lights on the floppy come on when the disk is trying to be read but can't read anything. It always asks me to reformat the floppy. If I say "Yes" to the reformat, I receive a message that the disk is bad and can't be formatted (even with new floppys). Am using Win 2000 Pro. and have 3 partitions on my one 160 MB hard drive using Acronis partitioner.
Can I get some suggestions on how to fix this problem?