I have a radio play that I've converted from multiple MP3 tracks to a single M4A audio file using fre:ac. I can't tell it apart from the original files when I play it back on VLC for Windows or any other PC media player. When I play it on VLC for Android, certain sections are inaudible. I have confirmed that the file sizes are identical to the byte so I'm pretty sure it's not damaged, and just about every other part of the play sounds the same on both Windows and Android.
The play is the BBC Radio 4 adaptation of the Hitchhiker's Guide to the Galaxy, Tertiary Phase, and the "broken" sections are an effects-heavy voice, when the creature Agrajaj speaks. There's a conversation between two characters, and you can hear one set of lines, then a barely-audible bit of static or distortion while the opposite lines are read, then the first character speaks clearly, etc. It sounds almost as if every part when it speaks has been removed on purpose.
Could this be something wrong with the Android decoder, maybe? The only relevant setting I could find, changing Settings -> Audio -> Advanced -> Audio Output from AudioTrack to OpenSL ES, made no difference. I'm attaching the MediaInfo dump for the file, and can upload it somewhere for testing if need be.