It appears that Audacity assumes the first 2 tracks of a polywav are stereo. I wonder if there is a setting to not do that?
Reaper imports polywavs as one multitrack file, then you can use the menu, ITEM/ITEM PROCESSING/EXPLODE MULTICHANNEL... to separate all tracks into individual Reaper tracks. N.B. Reaper recopies the data for each track and makes a reapeak display file for each new track, but puts all this into weird places, typically the (Mac) user's documents folder. I haven't figured out how to get it to put these duplicates in the same place as the original, and of course, it won't open again without them.