I think, I found the bug. The variable DistOld should be in units of mm according to line 3206. However, in the function ParallelCyclotronTracker::checkGapCross it is computed in units of m. Therefore missing a factor 1000. I have to run some checks but including the factor removes these lines in configuration space.
The problem is that the RFCavity still uses units of mm and ParallelCyclotronTracker is partially changed to units of m.