If NMCI didn't absolutely suck, it would be OS-independent. This is the year 2008, shit ought not be tied directly to your operating system but rather your browser and the myriad of smaller plugins that it can run and support cross-platform.
Any entity that codes applications be it client-side or web-based for specific operating systems is shit and stuck in the past.
However, that does not solve your problem, sorry sir, just drunk ranting. It sounds like you need the correct root certificates for the CAC reader to correspond with said websites/portals however, I have no idea if NMCI publishes those - most likely not.