I'd never heard of a MB3 before, so I looked it up and it appears to be 100% identical in all but name to my MD3, what the difference is I have no idea!
Anyway, being the same as my machine, the toolchanger index is a very simple geneva wheel mechanism, so if it works flawlessly most of the way round the chances of there being something wrong mechanically are practically nil. Short of built up chips jamming the mechanism about the only possibility is that the magazine is not stopping in quite the correct rotation at certain positions and the index pin isn't locating properly in the hole. There are limit switches on the index pin so the control would fault out in that case.
If you're sure the problem is electrical, the best place to start looking is the decoder box on top of the umbrella. If you take the top cover off the tool changer so you can get into the workings of it, you'll see a small box with six led's on it, that's the 6 bit binary counter that tells the control where the magazine is. The led's should light up in the following sequence in relation to the position of the magazine:
Remember to use the diagnostics screen, it shows the status of every component of the toolchanger.