Apparently every problem can be attributed to a misalignment problem. The telescope has troubles with heavily misaligned DUTs. Was resolved by creating different gear-files for each run with pretty precise coordinates of the DUT position calculated for the telescope coordinate system.
Additionally one has to watch out for misaligned planes of the telescope itself. It was required to allow for more than 2mm offset for the telescope planes behind the DUTs. This can be easily checked by looking at the PreAligner plots in the -hitmaker-histo.root file.
It look something like this:
and not like this: