Well Mines been changed twice, second time I had trouble and had to get an apple autorized dealer to email apple and complain for the to change it again.
Here is an example of my one that is being changed at the moment (did exactly the same thing before, this is the second time its done it).
See the sort of brown mark on the laptop. Apparently they couldnt change it because of the little mark on the side (acually took a picture of the mark, but you can see the discolouration quite well on it from this angle).
Also, here is an extreme case of discolouration:
http://www.macobserver.com/article/2006/06/macbook.jpg
The guy who is now replacing my second top cover says he thinks its probably a case of apple using cheap or not enough thermal paste, as its either dried out because its cheap and nasty, or there is not enough.
Anyway, its being done and investigated as I type, and I get it back tomorrow morning, so will tell you have I get on with it then.