Hi Manxman, yeah, that's exactly my problem! In my case I copy radio plays from reel-to-reel to mp3. Though reel-to-reel has much more charm, the sound quality of the tapes (reels) decreases with the years.
WavePad has a strong recording performance: easy, quick etc. Editing both channels at the same time is fine too. It's only when it comes to editing only ONE channel (which is unavoidable since reel-to-reel recordings are never 100% balanced) where the problem starts.
I follow the next steps: first, I record my reel-to-reel to mp3 in WavePad, then cut the silence at the very beginning and after the end of the recording, together with some other editing, then save the file as mp3. Then I open my old editor, which is Audio Editor Gold, open the mp3 file there and edit the channel that needs to be edited (Audio Editor Gold has this option as a standard setting but the program is very slow and takes a lot of virtual memory; so I record in Wave Pad and then balance the channels in Audio Editor Gold).
I agree that this option should be standard in WavePad, but apparently people don't see the point.
It's not a very nice solution, but it works for me.