Confirmed as a bug, and a rather embarassing one at that.
The biggest problem I've had with this game is trying to find people to test it. You can imagine that by now, I've played more of this game than I ever cared to. I handed out copies to a dozen people and never heard about this, released it since they "didn't find any bugs", and one year later this post is the first I've heard of it.
June 03, 2013, 10:49:19 pm - (Auto Merged - Double Posts are not allowed before 7 days.)
Found the problem and have a fix for it. Insertion routine used to put the script back in for the last patch was wrong. Damn... full year and no one reported all the problems it caused. Emailing a fix to OP, will post it public after I get some feedback.