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That is a little odd. From what you describe Amadeus Pro can do a similar thing using markers to designate tracks inside of a larger file. I tried that some time ago and I found it a little awkward. I couldn't possibly have borked up the process. 
When I do this I select the contents of what will be a track, cut it out of the larger file, paste the content into a new track, and save was a file. I started this because I didn't quite understand how to do things reliably the way you do.
The up side to all this is that individual tracks are saved as separate files. Downloads from the iTunes Store and several other places are treated this way so things seem to be nudging me in that direction. Lol.

When I do this I select the contents of what will be a track, cut it out of the larger file, paste the content into a new track, and save was a file. I started this because I didn't quite understand how to do things reliably the way you do.
The up side to all this is that individual tracks are saved as separate files. Downloads from the iTunes Store and several other places are treated this way so things seem to be nudging me in that direction. Lol.