Same experience here and I don't have a good solution. What seems to work best for me is to use Presenter to make the recording. Take the audio file that Presenter creates and edit that externally. Then re-import. For some inexplicable reason, the quality is better than when starting external. Not much but a little.
Exactly the opposite of what I would expect.
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Have you tried converting the .wav to mp3 to see if there's any better performance with the audio file? I realize that it's not optimal (using an mp3 file) since Presenter is going to compress it when publishing anyway, but you may want to test to see if there are any significant differences as a result of importing a different file format.