I think I may have found the problem - fake DS3 controllers.
They look great, absolutely like the genuine article, but having a look at some YouTube videos they do have a few of the similarities described in some of the videos for fake controllers. For example, the top of the box they came in is light blue rather than the darker, patterned blue of a real box, approximately 1 minute in to this video
They also won't connect through the offical PS3 configuration in the menu - I have to use the Shanwam (is that the right word?) setup/driver to make them work.
When I plug them into my PC it says a PS3 Controller has been detected - would it say something else if they were genuine? Like DualShock 3 detected or similar?
Also, as above, they just don't seem to want to charge. Lights will flash when plugged into my computer using the cable that was supplied with them, but they never stops flashing, and its all 4 lights flashing rather than just one.
When plugged into the Pi they just won't stop vibrating either!
Girlfriend got them from eBay and while they look the part I'm convinced this could be the problem. Shame, as I don't really want to have to spend £50 a pop on DualShock 4 controllers!
Maybe I could get some battery packs and dig out my old Xbox 360 pads instead? They're great, but the batteries on them are dying.