I have a detector geometry with the following levels: World - Detector - Module (replica) - Plane - SCPlane - Counter(replica) - SCounter. The latter is sensitive. I hit a mu+ in the middle of the detector. If this muon emits delta electron in SCounter, after that aStep->GetPreStepPoint()->GetPhysicalVolume() returns me (on the next step) ModulePV instead of SCounterPV. For this reason the rest of step in SCounter remains undigitized. The corresponding code can be found in /afs/cern.ch/user/k/kirsanov/publis psgeant4.tar.gz. I took geant4.0.1 from the Web and compiled it on my PC with Linux RedHat 5.1. CLHEP i took from the Web and compiled (all this one week ago). I used file configure which is in psgeant4.tar.gz. Libraries are granular. The program i run like this: psgeant4 cardg.g4mac. I tried to remove ionization from poststep processes: the problem almost disappears (almost because there is also rather rare pair production).
The problem report was not misfunctioning of Geant4, but due to the user's misunderstanding.