...... I've finally found out that it is pinworm.
You might remember me asking about him getting yellow deposits around his anus and being generally itchy around the time he was due worming. It seems that pinworm has these exact symptoms, causes little internal problem and is treatable by normal worming programmes. Phew! (Although why does he still have the deposits a week after being wormed...?!)
http://www.equidblog.com/uploads/file/JSW-MA2%20Pinworms%20-%20Equine.pdf
Problem solved.
Catherine