The plugin code is removing the alpha when comparing colours, which isn't a problem. But its also removing the alpha when changing them - this is causing the issue I'm seeing.

Looking at the code, it seems I was originally concerned about preserving the destination's original alpha. Only if the new colour has a non 0xFF alpha, should the new alpha be used). I had disabled this as extraneous.

I've fixed the code, and re-enabled alpha preservation of the destinations original alpha. So far it looks good. Once I've done some more testing I'll put up a new version.