So, this may or may not work. By default, the ACIDIZE setting in BIAB is on. I would try turning it off and seeing if that solves the problem.
Just click on the "WAV" button in the topline toolbar, then select "Save all tracks as WAV file (with options)". When the screen comes up, uncheck the "ACIDIZE" checkbox.
If you do check the "DEFAULTS" button (to set everything back to defaults, you will notice that the ACIDIZE checkbox gets turned back on.
I could be wrong, but it makes me wonder if when BIAB generates WAV files (and doesn't give you the option of making these settings, as happens when you drag and drop), that it is using these settings to create the WAV file.
It's worth a try to see if this solves the problem.