What sort of uncomment behavior are you seeing? Does it throw an error and leave the text, or does the text get moved? For me, it will uncomment, but if you have a line that has to be shifted to allow space for the comment, the text will end up all the way in column 1 when you uncomment. Is that what you're seeing (comment mode = at left margin). Lines which have wide indent margins don't seem to be affected on a single line comment/uncomment.
As far as the lowercase issue, that's happening in setting/restoring the settings. I'd like to fix that, but I need to poke at it a little more to make sure my fix doesn't break something else.