I found some other strange behavior working with collimators (but not with the test example I uploaded here). I start with a beam of 10'000 particles which have a gauss distribution. I have a vertical collimator and a probe in front of the collimator. If plotting the tracks, I see that there are some particles hitting the vertical collimator, but they are not registered in the collimator.loss file. This is a plot of the profile:
However, if I make the collimator thicker (10mm instead of 2mm), some particles are now registered in the collimator.loss file. It looks like this:
The red points are the coordinates from the probe.loss file, the green dots are from the collimator.loss file. You can see that some, but not all particles are now registered in the collimator. I thought it might be a problem with the time step, so I increased the number of steps per turn from 5'000 up to 100'000, but the particles are still not registered in the collimator.loss file. This behavior happens no matter if I use PARTICLEMATTERINTERACTION or not.