My understanding is it's per room. Here's the wording from the rules. Given each unit is a separate reservation I read it as per reservation.
TRANSACTION FEES AND PROGRAM COSTS. Beginning January 1, 2008, DVC Members will be charged a non-refundable $95.00 transaction fee per Disney Collection (excluding Disneyland® Resort Hotels in California) confirmed reservation, which is payable at the time of confirmation. Costs of cash reservations, if any, are also payable at the time of confirmation.
I asked this specific question when I bought last week and was told by my guide that if the rooms are linked on the reservation it is one $95 fee. I hope he was correct.