I think it may be related to which telephone module you have, there is some information here:
http://www.myturbodiesel.com/1000q/a5/VW-bluetooth-FAQ.htm
Although it does say if all versions work with the iPhone, mine is a 2010 model, but has a retrofitted Bluetooth module, which I bought through a group buy here and it works with my iPhone 4S. However it did take two attempts to get it to pair with the Bluetooth.
Havent looked at the link yet (just getting ready for work), but i believe some people over on the Skoda forum have changed there modules for newer ones... This might be the way to go, think they are about £100 (on ebay anyway). Might get a price from VW as well..