I would venture that the desktop app is not puroposefully trying to grind the floppy drive. It is probably polling the OS for removable media (i.e. a Kobo) and a side effect is that the OS attempts to read the floppy drive and, presumably, since there is a no disk in the drive it waits until the drive times out with an error.

If the grinding puts you off just throw a floppy disk in the drive so that the OS will find something.