I'm sure this is a software problem as you suggest but some years ago
on our Tracermass we had a similar problem with Minor 1 cutting out
unpredictably. This turned out to be caused by a screw which had
vibrated loose within the collector housing and was shorting the
middle collector to the housing. Due to the housing being circular the
screw rolled around and sometimes rolled away from the collector
resulting in the beam reappearing - this rather depended on how heavy
the operator was and where they stood on the lab floor!
Darren Sleep GIBiol
Stable Isotope Facility
CEH Merlewood
Grange-Over-Sands
Cumbria LA11 6JU
UK
tel +44 (0) 15395 32264
fax +44 (0) 15395 34705