I remember reading something about this a while back. It has something to do with the subframe, either its bad, broken, worn... i don't really remember. I don't think its THAT huge of a problem though. Probably will get worse though.
Anyways, i have the same problem, so i know what ur talking about. It only happens when engaging first gear and comes from the middle of the car. I've had the problem for about 6-8 months now though.
I heard if you hold down the clutch for 5-10 seconds before engaging the gear, then you wont get the clunck. I think that might work, but for me i've just stopped worrying about it, and just engage normally and keep driving.