FAT conflict in windows

Dear gurus,
I earlier had win95 with FAT 16 system and later upgraded to win98 and now to winME. I now find that I am unable to save data to the floppy and also unable to format a floppy disk through windows. No problem formating or writing data through DOS (not windows DOS program). Attempts to format through windows yields a message saying unable to write FAT. Attempts at formating using a third party program indicated that there were two FAT systems that are conflicting. Any solution to getthe system to write to the floppy through windows is most welcome. Thanks LG