Weird thing: I made a movie in PrE 14 (for Mac, using OS Mavericks then Yosemite) using stills, videos and audio files. This was labelled "W....prel". Some of my audio files were .mp3's and some were .m4a files. I made the movie successfully and exported it to my desktop as an .mp4 file and then on to iTunes to be played on my Apple TV. Worked just fine and still does. Then, today, I went back to the another original .prel file (labelled "W.. 2.prel" to distinguish it from the first .prel file cited above) to add in an introductory video/audio clip imported as an .mp4 file, inserted it in to the beginning of the movie, and the re-exported the project back out as an .mp4 file to be played on my Apple TV. Surprise!....the audio portions that were in the .m4a format were empty (silent....no sound). I went back into the original .prel file ("W...2.prel) and, sure enough, those .m4a files were empty too!! Moreover, the original .prel file (W...prel") also showed the .m4a audio files empty!! I don't get it...........anyone else seen this?
I finally found an answer: One must rename the "name.m4a" file to "name.mp4". Then one can import that .mp4 file into the PrE 14 project and it will have the audio contents in it. That still doesn't explain why the project was OK the first time I uploaded it to iTunes a while back. Maybe it has to do with that fact that I was using OS Mavericks at that time whereas I'm now using OS Yosemite......don't really know.
If those m4a files are music, audio and video you got with iTunes, that would explain a number of your issues. iTunes media has some powerful copy protection software built into it that can cause all kinds of grief for video editors.
If, as I advise in my books, you stick with WAV files and occasionally MP3s as your audio and music files, the program will perform so much more efficiently and much more bug-free.