Depends on how you mounted the stuff. See ctrl-f4 in the readme,
along with mounting floppy images.

It uses multiple cd roms not floppy disks.

wait for the next version. (if you use isos)

else mount all cdrom at different drive letters.

im only finding that problem at the switch when taking the ornithopter for the first time from the tower fortress to the temple. im using dosbox. i didnt have any problems with the switch between the lab to the beach.

are there any save games anywhere online that can be downloaded to overcome this issue?

or is there a quick fix

nevermind i found some save games at
http://www.nicouzouf.com/en/?id=lighthousethedarkbeing

That means i don't have to make multiple drives oe use iso. I can just download a save that is right after the disc change so i can just quit dosbox when i need to change disks and get a game save right after the disc change.