I'm running audacity on a fedora core 2 system.
I opened audacity, default project rate 16/48. Imported a 16/48 wav, exported that track to another file name. cmp verified that the two files were identical.
It was a quick test and far from exhaustive, but proves that audacity (in my installation) does not massage the file when saving.
Edit:
For grins, I installed audacity on a win XP machine and operated on a 16/44 file running the same test. The saved files are different from the original and from each other.
Wow, sucks to run audacity on windows I guess.
Edit 2:
Thought about it for a minute then checked the audacity preferences. The default setting for quality is 44.1k and 32-bit float. I set the default bit depth to 16-bit. This solved the problem. Saved the track twice, tested both saves and the original against each other and of course they are perfect.
It's not just the save function that is affected, it's import as well. When you set the project quality to 32-float, audacity converts the 16-bit integer value to a float for it's working project values, then back down to a 16-bit integer on export.
So change that setting and you should not have this problem anymore.