The Agilent Account Manager came by to inspect the pressure gauges because they read over pressure when the pressure is normal and they pressure seemed to go down even though everything was off. Nothing much came of the visit, but he will forward along the latter issue.
The pressure after the weekend was 1E-3 Torr. There at least isn't a major leak then. I vented the system (both the turbo and the main body of the chamber) and pumped down with the scroll. I turned off safe start as the turbo has been lubricated by being on recently. At around 1 Torr, I turned the turbo on and it increased up to its final speed in under a minute. After a few minutes, the pressure was in the 1E-6 range so I turned on the ion pump. The ion pump behaved as normal. The RGA showed a decent amount of H2 and was ~2-3x the reading of the Agilent pressure gauge. I closed off the gate valve to the turbo and turned off the turbo. The pressure rose by quite a bit to 1E-5 Torr and I decided to turn off the ion pump and RGA. I think we need to wait until the pressure is closer to 1E-6 Torr to close the turbo pump. After turning off the ion pump, the pressure rose to 1E-3 Torr in ~10 minutes and then stabilized. I think this explains why the pressure was so high last Thursday. I still don't know what caused the ion pump to go off. Hopefully the ion pump is ok.
Around 4:45 PM today, I vented everything and pumped out with the scroll and then turbo. I turned on the ion pump around 4:55 PM. By 7 PM, the pressure should drop to 2E-7 Torr. If not, then something is wrong with the ion pump, or something is wrong with the all metal angle valve, RGA, or the connections between them. Closing the valve to the RGA would be a good check.
Sometime in the last 40 minutes while I've been standing next to the pressure gauge output, the ion pump turned its self off. I never noticed any spike, likely because the turbo is on. The ion pump turning itsself off and outgassing would explain the whole issue from last Thursday. I turned on the ion pump at 5:32 PM when the pressure was 1.2E-6 Torr and the pressure didn't go up; it actually went down to 9.8E-7 Torr in ~30 seconds. The ion pump controller BNC voltage is 3.50 V. Maybe we need to keep the ion pump gate valve closed when venting. I will keep an eye on the system for the next few hours.
The system reached 3.9E-7 Torr at 7:07 PM after some RGA testing. I shut the gave valve to the turbo and turned off the turbo. I then turned off the scroll. The pressure is 7.5E-7 Torr at 7:11 PM. This is much better that earlier today, emphasizing that the ion pump needs to be pumped out for ~1 hour if it's vented to atmospheric pressure.