Sounds like you need to comment out the /dev/fd0 line in /etc/fstab.
/etc/fstab is the file that tells linux what to mount on bootup.
Since I don't use X-windows often, I'm not sure if there is anything else you would need to change.
Sort of sounds like there might be a cron job that periodically checks for the floppy drive.
You could also try running kudzu to see if it will remove the reference to the floppy.