Here's a funny one..

I've written a port Scanner. It works fine when scanning over Wifi, but it behaves differently when in 3G mode: Everything returns a false positive.

What would cause this? Is the mobile network doing something to the traffic?

Probably because you isp blocks every port automatically, or because on 3G you are behind a NAT. 3G and Wifi are indeed very different . Your 3G provider probably is restricting your 3G access very much, in contrast to Wifi, which you are to do what ever you want.