I have not heard about this particular problem concerning Color Navigator and Snow Leopard.
There are some issues with SL though. All the different monitor profiling software packages have similar issues with not being able to identify or find the default monitor profile in the new operating system. Sometimes this takes the form of showing a calibration reminder every time you log on (even if you just calibrated).
When calibrating this monitor you should use the Color Navigator software, not the i1 Match software. CN will allow access to its internal graphics in the display itself which makes the profiling much more precise.