I'm typing this with the green-on-black skin on. It mostly works now, if you make sure that in your Monobook.js the variable Gerbrant.hidePane is set to the following value:
 {
     background: "#000000",
     color: "#00dd00",
     selBackground: "#00dd00",
     selColor: "#000000",
     borderColor: "#00dd00"
 }
You can for example wrap it in the following, or any other way that's okay in JavaScript. (The rationale behind this settings scheme is that I use various scripts, some of my own, some of which have settings, and some written by others, which may have settings as well, so I wanted to be sure settings for my scripts are in a seperate namespace, where they can't touch or clash with those of other scripts.)
 Gerbrant = {
     hidePane = ...
 }
I may need some time to iron out a little bug, but at least it works. As for the other problem, this is caused by the script's (i.e. my) assumption that either the interwiki list or the toolbox is the last menu. If this isn't true for some reason, things can go wrong. I'll try to fix this if I can find a good test script to work with. Also, if you have suggestions for better colour values or a good way to automagically detect common colour skins like green-on-black so I could select more appropriate defaults, I'd like to hear them.