Created attachment 262 [details]
Macro file with line that solves the problem

TestEm5 in MT mode shows that the activation of em processes like PIXE via UI commands does not work. The following three lines:
/process/em/fluo true
/process/em/pixe true
/process/em/auger false
Are not taken into account.
This is because in MT we need to force the trigger of re-configuring physics. Adding the following UI command makes the example work (as in the attached macro):
/run/physicsModified

A possible solution would be to add 
G4UImanager::GetUIpointer()->ApplyCommand("/run/physicsModified"); 
To messengers that define commands that change physics (like the three discussed here). This strategy is already applied for other UI commands, but not for these three.

Andrea