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I don’t have a solution for this, I fear, but want to report that I’ve been experiencing similar behaviour myself, if I’m not much mistaken (and posted regarding it, for that matter, although I’m afraid that I didn’t keep up with that thread): once compiled into a p3d file, certain lines in my prc files seem to be ignored (screen size and fullscreen mode are two that I’ve noted), while others seem be respected (such as setting whether the window may be resized). This behaviour doesn’t seem to be limited to my own computer.
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I believe that packp3d doesn’t by default include multifiles; however, you should be able to instuct it to additionally include files of specified extensions using the -n and -e flags to packp3d–the former specifies an uncompressible file type, while the latter specifies a compressible file type.
While I’m not sure that I’m correct in this, I believe that I’ve packed multifiles as uncompressible files.
To give an example:
packp3d -o appName.p3d -d someDirectory/anotherDirectory -n mf