Thanks for the suggestions guys. I've narrowed the problem down further. The machine in question runs without a monitor, keyboard and mouse, mainly because its used as a download box.
When I either shut down the machine or restart it via remote desktop, it won't connect to the network once restarted. To solve this, i have to connect a monitor etc and open IE and that solves the problem - it can be controlled via RDP.
Is there any way to solve this? I may need to shut it down to install updates etc, and I don't want to be connecting a monitor etc every time.