1. inkapp.png is still smaller as a png, so it can't be converted (well, it could, but the plugin checks for filesize and skips conversion if the new images is larger than the original).
2. terraorba1.png was better as a jpg, but I had no trouble converting it on my dev site, naturally. Replicating these types of things is very tricky. I really don't doubt that there could be a bug, as there's a lot of code involved, and I'm only human, so I don't expect perfection...
3. juxgrid.png was another one that had transparency, there was just a small transparent border around the edge, so the plugin would skip this one as well unless there was a background fill color entered in the settings.
So, here's what I'm wondering, can you try this (which should replicate what you did originally, if I'm understanding correctly):
1. Disable the optimizer plugin.
2. Upload 10-15 screenshots that you have original pngs for. Alternatively, if you left the originals in place on the server, you could download those to your computer to use for this test.
3. Enable the plugin.
4. Make sure PNG to JPG conversion is turned on, as well as debugging, and then run the bulk optimize for just the new ones you uploaded (you can use the Bulk Optimize from the actions menu on the Media Library if you hadn't discovered that yet).
There will be debugging info output for every image run through the bulk optimizer. So, if they don't convert properly, copy the debugging info for one or two of them (might want to use pastebin.com for this), and we'll see if we can spot anything amiss.