Two flights today in 1997 M20R. 20 minutes into first flight felt a "bump". It felt like like the engine missed, no indication on engine monitor of anything amiss. The remainder of the flight was normal and I wrote it off. Second flight was similar but when the "event" occurred, the rear seat passenger reported a thump from under the seat. It was a 40 min flight but felt the bump two more times. Lowered the gear early and no issues. Thought I may have an issue with a gear door but everything was tight on inspection...Again, nothing unusual on the GEM or other engine gauges. 3000 hr in the "R" and never seen this one...any ideas on where to start would be greatly appreciated.