I did not test it to see if manual frame skip settings helped before, but the poor frame rate with auto frame skip has always been there on the games I tested, in every release you have made so far (that I have used).

True enough, but I was just a little surprised that it was enough to upset the sound.....

I didn't know the specifics but I knew it must be problematic emulating the sound on Amiga because sound buffer issues has been the biggest problem I have had in WinUAE. For a long time it was a trade-off between glitchy sound or a larger buffer with delayed audio.