Do not be alarmed if your subwoofer makes a "thumping" noise.
Basically, when subwoofers start up, the capacitors in the amplifier charge up and are then able to be used in powering the woofer. When the subwoofer goes into standby, the charge stored in the capacitors is discharged, usually causing the sub to "thump". If you watch it, you will see the Power LED on the subwoofer turn off when this happens.
MartinLogan subs have an auto-on circuit to kick the sub on when it receives a signal, and shut down (after a period of time) when that signal stops. To keep it from shutting down when there isn't very much bass, such as a dialog heavy scene between action scenes, there is a roughly half-hour delay (varies by product generation) before going into standby. This is why it happens a while after the system has shut down. This isn't exact, it is usually 20-40 minutes after the sub stops receiving a signal.
The volume of this "thump" seems to be tied to the volume setting of the subwoofer, so one thing you can do to minimize this sound is to go into the settings of your receiver/amplifier and increase the output to the sub, then turn the subwoofers level control down to compensate. That way you get the same output from the sub, but the thump may be quieter.
If you are getting several thumps in a row, or unusual, growling noises during play, that would be an indication of an issue, but a single thump as this goes into standby is normal.