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You can publish an EXE for PC and then an App for Mac from your flash. Then, using toast, you can create a hybrid CD. This will only show the PC contents on a PC and the Mac contents of the CD on Mac, keeping them seperate. I am not sure if you have a Mac or PC, but you will need Toast to achieve this. I am not sure if Nero or Roxio can do this.
You could also leave you published file as an HTML which will work on both platforms (but the user needs to have flash player installed). eliminating the need for a hybrid disc.
Rafa, that will probably be the route I'll take. I still wish there was a way to hide or package all the external files. Its not bad if the person looks at them, but it just seems cleaner to not have a bunch of folders and external files next to the launch executable. Thanks for your help