Hi there,
After calibration of a network analyzer I always do a simple check with a 3dB attenuator: should measure -6dB Sii when connected either to Port1 or to Port2, and should measure -3dB Sij and Sji when connected between Port1 and Port2. If this doesn't work, then no point going any further...
It could also be a problem with the trigger if your measurement is pulsed. If you use Agilent 8753 series, the trigger is done on the falling edge and doesn't work above 50Hz...
Mosieur_Oiso