Is the thunk-ing sound successive? That is when you start it up do your hear a "thunk thunk thunk" or is it just something more like a loud "THUNK". How long does it last? Just for the time it takes to start the car (key in "start" position)? Is it after the motor is/while running?
You could try and remove the starter and test it electrically (be very careful doing this and make sure you know how to test it before trying it yourself). You can just try replacing the starter with a new one. These should rule out the starter making the noise. Most likely it is something inside the engine, perhaps the gear on the starter is worn and the engine is slipping when starting. So you can check that area, the interal components.
It could also be something as silly as a missing bolt or nut and the start up of the engine is knocking around something loose, or even the engine isn't properly mounted.
I am not that familiar with the problem so to me it can be a couple of sources. I would try and rule out a few things as well to help narrow what I'm looking at (or for). For instance try having someone start the car as you pop your head under the hood (careful!) and try and locate the exact place the sound is coming from.
