Home Theater - Random Thumping from Subwoofer

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Any ideas what could be causing that?

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Probably rap music.

Driver bottoming out? Adjust the volume on the sub and see if it goes away.

RCAs being loose can do it, speaker wires/connections can do it. Those are just the simple things to check

Hammertime's suggestion is true. Check the RCA connection. Cables do fail sometimes--and usually it it always at the connection (the barrel). Also, this is a long shot, but I had something similar happen to me--is the cable to the sub a good shielded cable?

I once heard a "Rrrrrrr,Rrrrrrr,Rrrrrrr,Rrrrrr" sound about every second coming through my audio rig. It would only happen sometimes--drove me friggin bananas trying to figure out the cause.
Eventually I did find it--Mrs. Esquandolas was on the other side of the house on the treadmill (a pro treadmill with a big arse motor). Every time her foot landed on the track, it stressed the motor just a tad (every step), and this was being transferred through the electrical grid of the house and the cable to my turntable was picking it up! Change cables--it stopped.

OR...if it has an internal amplifier, it could be going bad or have a bad internal connection, pull the amp out of the cabinet and check it out.