Looks like the game must have been updated or something, but it made my save file (and others' apparently) weird. Solved puzzles are sporadically gone, and I have a couple shown solved that I never did.
Cool game, but it was first done in one of the Dr. Brain games made by Sierra, I think it was Island of Dr. Brain.
Also, none of you people complaining about the limit on the number of directives would have ever survived programming 30 years ago. Programmers these days are wusses.