User friendliness is kind of a subjective thing. Personally, I don't find the Export dialog confusing, but the "gotcha" for me has been having a section of a track selected (usually off-screen) because of an edit or looping a part. Not really a big deal, since it's obvious what the problem is when my export only takes a few seconds.

But I do think there's room for improvement there, and I believe Noel said they're looking at some changes.
To the OP's problem, I'm seldom surprised when an export from any program doesn't work as expected in another program. It's a pretty rare occurrence, though.
Not sure it would make a difference, but I would have turned of the 'Save ACIDized' and 'Save slice markers' options (as I mentioned in post #10) and re-exported. Dunno why you would leave those on if you don't want your file to time-stretch/loop.