The short story: I'm using Audacity 1.3.5 beta and noticed that if I drop a 16/44.1 .wav on it, then immediately export that to .wav without doing anything else, the resultant .wav is different than the original (as checked with Foobar's bit-compare tool and EAC's compare wav tool).

That seems wrong. Shouldn't doing that be equivalent to just duplicating the file?

I think Audacity converts anything into its native format. I would try changing this native format to match the input file format.
Edit->Preferences->Quality, there you can set it up and possibly turn off dithering as well.

Ah ha! The issue is the dithering. I had already tried changing the default format to 16/44 but that didn't help. I hadn't thought of the dithering, though. *slaps forehead* heh

Thanks for the help, Martel.


Edit: clarity