"Seems to install okay", but you didn't say if it runs okay.
If your app needs those files and they are not anywhere in the bar file, the app surely can't work. It can't magically reach out to your desktop machine and grab them or anything...
More likely either they're simply in another directory of the .bar file, and your app is actually looking for them there even though you didn't realize it, or your app simply doesn't need them to be there as separate files.
Did you by any chance use the Embed metadata tag on them? Or is this app all done with MXML stuff and maybe that pulls them in for you? (I'm not familiar with the MXML "stuff" so I have no idea if that's how it works.)
