Bryan,
I did not work on Optima, but the problem seems to be similar I
experienced a few years ago on my Russiam MI1305 machine. It is true,
as suggested by Stephen, that there should be no pulasation in the
isotopic ratios if the machine is linear in a given range of
pressures. It is probably not the pressure variation that causes your
problem, but pulsation of one of supplies. The beams do
not really change their currents, but they are pulsatively shifted at
the collector slits, what may cause changes of isotopic ratios due
to different plateau lenghts for different beams. Pulsation in the
high voltage supply could cause this effect. You may also look
at other ion source supplies, like electron acceleration voltage,
correction slits voltage (this usually comes dividing the HV) etc.
Regards,