When the vacuum pump is running, it is trying to reset the vacuum on the system. As Brian said, it sounds like you have a vacuum leak somewhere, which can be as simple as a dirty seal. Make sure the bowl seals are not obstructed by matter or toilet tissue by turning off the system, holding the foot pedal down, and running a brush or cloth around the seal to clear any obstruction.
Make sure you use plenty of water when flushing (hold UP on the pedal to add water), don't overdo the toilet paper and be sure to use a type that disintegrates rapidly. Then use the proper "technique" to flush as described in the manual... press the pedal for at least THREE seconds when flushing, then let the foot pedal "snap" back into place. Don't "ease up" on the pedal...it needs the snapping motion to help reset the seal.
Make sure the ONLY things that go into the toilet are bodily waste and soluble toilet tissue. No feminine products, wet wipes, etc. should ever be introduced into the system.
We have had three years with no major problems, though there is a learning curve. Last summer we learned that traveling to high elevations (over 8,000') will cause the pump to run significantly longer to reset the vacuum.
It takes a little getting used to, but the vacuflush is a tried and true system used extensively in marine applications. Hopefully your issue will be easily resolved, either by you or the dealer.
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