mguertain, I'm a PC guy and don't pretend to know anything about Macs, but it sounds to me like you've got a video card/driver problem.
The differences you cite in the two monitors aren't really significant, and the purpose of calibration is to make everything look the same regardless of hardware differences, anyway. It sounds to me like either your card or your driver or the OS isn't accepting both calibration profiles, but instead applying one of them to both monitors. Have you downloaded and installed the latest drivers for your card? The ATI site says your card has dual LUT's so you shouldn't have a problem if you have the current driver for your OS.
I've run two monitors on my PC's for more than two years now, two different monitor setups on two different PC's, both using ATI cards and have had no problems calibrating with a Spyder2. I recently switched to the i1D2 and again, no problems.
In Windoze, I have a primary display channel and a secondary. I can access either and set the default profiles through the OS, I assume you can do the same with the Mac. The profiles you create with the i1 should have different names, can you find them and associate them with their monitors and do they stay associated when you go back and check after a reboot and see which profile is tied to which monitor?
What you're seeing shouldn't be happening. Maybe you could disconnect one monitor temporarily and see if you can get a good calibration on the active monitor. If you can, I wouldn't think the i1D2 was the problem. If you can't, it's obviously bad. If you can get a good profile on one and not on the other, it sounds like a hardware/driver problem to me.
Maybe some knowledgeable Mac person will chime in.....