Re 2001 Mazda Tribute, old keys no longer start:

I have four keys which worked in 2002, two of which I programmed by the book. Now all keys will open the door but only the one key I always use will start the engine. After I try to start using one of the others, my good key not start for 15 minutes. Scary!

When I asked the local dealer in Eugene OR, he does not know about this problem, but he will reprogram all keys for $88.

How can I understand this, and what can I do?

Thanks.

p.s. Any advice for souping up a 2-liter engine?
p.p.s. Does anyone advise against installing a third-party cruise-control on a stick shift?