My guess would be per night, regardless of what the base rate is. Otherwise if you stayed a single night with a free night cert, you could get any standby upgrade for free. On the actual page, it pretty clearly says it's a per night fee I think.

I'm doing a buy 2 stay 3 rate at the Hotel Vancouver and was offered a standby upgrade to a Morningside Suite for $150 (!) a night. I would fully expect to be charged $450 if I accepted the upgrade.