Do you have good clean Helium for carrier gas? If so what flow are you using?
Helium purity 99.995, flow 0.5 ml/min.
Definitely have a huge amount of air coming in somewhere. If I remember the GCD has the same analyzer setup as the 5971, which means you have the fairly wide rubber gasket between the top plate and the analyzer. If even a piece of lint gets on those you can get an air leak. If you have some Apeizon L grease, coat that gasket with it, then use a lint free Kemwipe to remove all but a very light film, then replace the gasket on the analyzer. I usually wipe the surface again with a Kemwipe before setting the top plate back on and when I place it on I move it slightly side to side to make sure it is sealing well. You may also want to do the same thing to the o-ring gasket on the vacuum interface.
I had a co-worker once who had a really bad leak in a 5971 and when we opened it back up we found a hair lying across the gasket, removed it and the leak was gone. It doesn't take much on those instruments to cause problems.
Seems I can shut up MS interface by usual needle and re-tune device in order to check whether it's leaks or dirty carrier gas?
Once the leak is fixed, re-tune and if the multiplier is still 2000 volts or above, I would consider replacing it.
Do you mean that excess air in detector can be a reason of so big voltage on electon multipier?