Likely the engine surged due to either bird strike or inlet distortion; the booms you heard are characteristic of surge and happen at a periodic rate.
Usually spectacular and may be accompanied by compressor coming apart, but transport category engines are certified to contain the event.
Too late to be a bird strike (unless, for some reason, the jet startled them).. The booms (lots of bass), were about every 5-8 seconds (estimated)..
Glad the troops got back to the ground safely!