To see a description of the problem check out this old post.
Mac OS X Your network has been compromised
It appears one of the latest updates to Mac OS X has fixed this problem. I can now have my MacBook remember networks that have multiple access points under the same SSID.
I think the specific update that corrected the problem can be found here AirPort Extreme Update 2008-004
This has been a problem since around the First of 2008. Little bit slow on the old repair.