How do I save the master section for each .wav file?

For the location, see this:
2013-10-06_19-33-07.png
You need to explicitly load the associated Master Section preset by clicking the load button (if it was automatic, what would happen if you would load 10 files at the same time…).

Note that WaveLab 8 has a new Master plugin section, stored with the audio montage, that allow the montage to stored all the needed parameters in a single file. As what you are looking for.