After uploading it to my server, I've verified what I suspected. The fault is not with the plugin, it is actually native to wordpress (the GD library used to generate thumbs more precisely). I believe it has difficulty with 8-bit PNGS, usually that is in relation to transparency, but perhaps the difficulty is that wordpress never bothers to check if a PNG is 8-bit, and just mangles all the thumbs to 24-bit regardless.
Unfortunately, it doesn't appear that either optipng or pngout attempt to downsize them back to 8-bit, so you'll want to see if you can find some utility to take care of that for you. pngout is able to save some extra space if you crank it to the lowest setting, but unless you're on a dedicated server, I would avoid that. optipng only manages to scrape off 2 bytes at max settings, so that's not worth much. Both of them fully support 8-bit PNGs in my testing, so that fully confirms that the blame lies with the GD library that does the resizing.
I'll take a look at the ftp uploading issue here in a bit.