As others have said, it's usually an annual excess per condition.
For example, William has dry eye, an ongoing condition that needs eye ointment every day and vet checks every few months. My insurance year runs from August and in the year that started in August 2009 I put in a claim for dry eye treatment in January 2010 and paid the £50 excess. I put in a further claim for dry eye treatment in July 2010 and didn't have to pay an excess then because it was for the same condition.