If the floppy had a valid filesystem on it already, Mandrake might be auto-mounting the disk (via Supermount, perhaps?) when you insert it.

Did you insert the disk prior to running the mkbootdisk program? If so, try waiting until you get the "Insert a disk in /dev/fd0..." message; that might catch it before the system has a chance to automount it. If that doesn't work, try unmounting the floppy before running mkbootdisk.