Dear Paul Dennis,
We never faced such type of problem. But few things could be done to know the
causes for it.
1. Try to run same gas as standard as well as sample.
2. Adjust the pressure on the capillaries (SA and ST sides), so that the flow
is similar in both sides under similar conditions.
3. There could be some problem with filament. It could be replaced.
4. The last possibility is to check electronics, especially of Faraday cups
amplifiers. But it is really hard to pin point about electronics faults.
Good Luck
Mahendra