Hi- I am running a Varian 3800/4000 GC/MS system. It's been on but out of daily use for a couple years and I am starting analyses back up again on the system, i.e. all methods have previously run and were optimized for the instrument.

I have run some standards in our "full scanning" methods and they run just fine (retention times haven't even shifted since method last run in 2012!!), but when I switch over to SIS methods (updated, based on the new full scanning methods), the system sits under "Equilibrating" for ages. All lights on the GC control panel are green and say "ready" as well as the MS, which says "ready". I can't figure out why it is still "Equilibrating". Full scanning methods download and "ready" within a minute or two. All conditions except for SIS vs full scanning are exactly the same for the two methods. We do have an uninstalled FID column and detector on the system, but I have taken extra care to make sure that injector and the FID are turned OFF on the method.

Any Ideas?