not sure with flash but with director
Im not totally sure how everything will work with flash im a bit rust with that program, but with director I was having the same problem getting it to load different files and working on the mac but not on the pc.
Some things to check:
PCs and Macs have different file paths, so make sure yours are relative, if not set a search path up somehow.
If that doesn't work you can use toast five to burn two seperate partitions on the same cd one mac and one pc so that they work on the same cd.
hope that was of some help.