@tamartin and I discovered this serious bug in
runbatch.py - it was only setting EvtMax and SkipEvents when they were provided at the command line. Any attempt to set them in athenaCommonFlags was ignored.
Additionally, add code to TrigMT_Reco_tf.py to set athenaCommonFlags properly.
Lots of test references will need updating...
EDIT: not sure this is the best way to proceed, see ATEAM-541