Compressor won't save a whole file.

I'm editing a small music video for a friend, and he sent me an mp3 to edit to until he can get me a higher-quality track for the audio. The problem I'm having is that I've attempted to up-convert the mp3 to a 48kHz AIFF file, and it completely lopped off the last 18 seconds or so of the track. First I thought he just sent me an mp3 that was already truncated, but it's not. I checked my copy of the mp3 and it has the whole song. The problem is that Compressor exported 3:25 of the 3:43 track length.
I deleted it and tried again, twice, and it did the exact same thing, twice. This just doesn't make any sense to me, and maybe someone here knows what I can do. I know I can probably make the sequence's audio settings to 44.1kHz and it'll probably work, but I'm more interested in why this program would truncate a file like this.
P.S. Does anyone else not really like the interface in the new version of Compressor?

Thanks for the reply. I tried QT and strangely, the first time I did it it failed, but then I exported it (without changing the name this time), and it seems to have worked. The only thing I did differently than all the other times (other than use Quicktime) was that I didn't change the name of the file. Maybe Compressor gets picky if you use a slash in a file name? Only thing I can think of.
Also, I had already checked to see if an out-point had been set, and there wasn't one. It would play the whole file in Compressor, so I have no idea what it was doing.

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