I can confirm the processor-count system, as that is how our maintenance contract with Rockwell works. We are in the "under 10 processors" category, which makes our E-Connect contract about $500 per year. I really only use it for software updates.
As I understand it, more PLCs installed = more money for support. I can't see any easy way around that since your distributor tracks how much hardware you buy from them.
-John
P.S. To answer the poster's original question, I don't think there are any extra fees or penalties to start a new support contract. Ours had lapsed for a number of years but was still only $500 when we renewed it.