I've been doing a lot of reading, it seems there are a lot of iPhone suffering this issue, and its not just with the Fiscon kit, VW kits and others all have issues with iPhone. From what I read though its just the 3GS that has probs, the 3G and 2G iPhones are ok.
It looks like it can be fixed if the iPhone is connected using the iPod cable, but whats the use in that. It seems that when the phone is switched off into standby using the off switch at the top of the iPhone then randomly triggers the iPhone into thinking that it is not needed so turns it off/on or something along those lines. Another iPhone app that can be used that pings an always on signal to the phone is an app called Insomnia which will help, that though will drain a bit of battery life.
I hope apple sort this with an OS update.