Although it's been a long time since my post about the Split-Flap Display and I didn't got around to make this post in a while, I finally managed to hunt the bug down I described in the post before.
As you may remember, I got two problems with the Display. The first was that some of the modules just died randomly and didn't respond to any signals. The second was that some of the modules have a small offset. Also there were a few modules that would start rotating on command as they should, but won't stop until disconnected from power.
But I can finally say that I have found the root of all the problems and now know how to fix them.