Troy,

The vacuum pump in the back of your car is used for the vacuum locks and for the vacuum controlled heater/airco system. The vacuum pump will only react on the door locks after opening and closing one of the front doors, trunk lid, remote control or dash switch.
If the vacuum pump is activated during the drive, it is probably because the heater system demands additional; vacuum to operate one of the vacuum pods in the heater system...I think you have to look into that in order to find the problem.

Take out the right upholstery in the trunk and have a look at the vacuum hoses on the vacuum pump. You can take out the vacuum hose to the heater system (probably a white hose/the yellow hose is for the central locking), blind it and listen to what the vacuum pump will do during the ride...

greetingz,

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1990 300SL-24
1993 C250D with a minor 600+k kilometer
www.MBenzNL.com(the Netherlands)