We're not sure what's causing it. The vet has put her on very strong anti-biotics to see if that will clear them up and it's working. If that didn't work then he said he would take some hair and skin samples to see if it's mites and then last resort would be food. He recommended cutting down on the different types of food she has as a precaution, I mentioned she had chicken dry food and beef wet food. He said beef contains more allergens than chicken so recommended cutting out the wet food. I doubt it is a food allergy which is causing this, I suspect it's more to do with washing powder (changed to fairy non-bio now) and febreeze (which I used to use) and then she just agrevated it by licking them.
She's still not slept yet today which she normally does over lunchtime, I think she's still trying to figure out how to get comfy with a massive cone around her neck!