Thanks for the welcome!
When we got our puppy check up at the vet, he got a dose of Revolution, this was Monday. Then I used a storebought ear cleaner Tuesday, and as of today there's no more head shaking and very little scratching (he's more concerned about being introduced to a collar around his neck now
!)So one of those must have helped with whatever the problem was!
Thanks for the advice though, next time I'll be more persistant at the vet when I notice irregular behaviour!