After upgrading to OSX 10.6 Snow Leopard, I've found some (all older than 10.5.4) programs behave oddly, and Cortex Command is one of them.
So far, all I have found in CC is that;
A) CC uses NSQuickDrawView, which is outdated, and
B) The mouse is no longer masked in windowed mode, and this is very irritating. it does disappear in fullscreen however.

I have not done much more testing yet, but feel free to expand on what I have found.