It sounds like your gauging is atmosphere referenced ("gage") and regardless of the resolution you can only measure the pressure relative to atmospheric pressure (hence the higher reading the longer the pump is working).
As you know, atmospheric pressure is changeable over a wide range depending on meteorological conditions, altitude above seal level, etc. You need an absolute referenced gauge ("0" on the gauge means no pressure or perfect vacuum). The thing you want to measure is pressure above perfect vacuum, not how far away you are from an imperfect reference.
As Richard noted, thermal conductivity gauges (thermocouple or Pirani) are commonly used in the range required for neutron generators. These are absolute gauges.
One final note, using grease is a common mistake. Unless you have a sliding seal (dynamic seal) you should never use grease. Epoxy is great for permanent or semipermanent seals; o-rings should be dry. Grease collects dirt, hair and gas and will cause more problems than it solves.
Steve
Created on Thursday, February 22, 2001 8:06 PM EDT by Steve Hansen