Without Normalize the sound is as in the real hardware. Normalize is a hack and will never work perfectly.
I did change the behaviour in Normalize in this release; it is now reset at the start of every song rather than only on a game change.
I may provide an option to tweak this in the next release. If what you really want is to record WAVs though, you probably shouldn't use Normalize anyway; get your favourite sound editor to normalize the whole sample equally.