I was also hearing a thump from my driver side at odd times for about a week after I got my car until I realized that the driver side window was not always completely shut. There was probably less than 1/8" gap where the top rear corner of the window was catching on the rubber above it.

It would tend to 'slap' shut sometimes and I was left wondering what the heck was happening. It was hard to notice from outside the car at first.

Probably not related to your concern but there you go.