First look the code is OK. But some notes are followed.
Victor

StiIstDetectorBuilder:

In StiIstDetectorBuilder::useVMCGeometry()

for (Int_t i = 0; i < M; i++) {
const TGeoMaterial *mat = gGeoManager->GetMaterial(map[i].name);

if (! mat) continue;
It MUST NOT be "continue". If no material it is disuster! It must be assert here.
=================================================================================

TGeoHMatrix *combI = (TGeoHMatrix *)istRot->FindObject(Form("R%04i", matIst));

if (combI) {
combI->Print();
}
Again, no matric(combi) it is desaster. Must be assert
=================================================================================

Again
if ( !p ) {
LOG_INFO << "StiIstDetectorBuilder::AverageVolume() -E- StiDetector pointer invalid." << endm;
return;
}

Again it is a fatal
================================================================================

if (!p->getGas()) LOG_INFO << "gas not there!" << endm;
Again fatal case
================================================================================
if (! nodeT) continue;;
It must not be silent continue. Assert is better