This is not a situation we have encountered before, but we can only assume that as the premium rate is calculated by the list price plus options, the dealer is reverting to the most recently-available list price for your car, which is over £40,000. Unfortunately the price you actually pay is irrelevant to how the charge works.

This certainly seems unfair, but there are few options available to you. We would certainly raise it with the dealer and ask for a written breakdown of how the charges have been calculated. Also contact the DVLA and ask them to clarify, although you may not get a satisfactory response.