Dollars to donuts says that its a certificate issue, namely a DOD certificate not recognised by a trusted CA. The only way around it is to make an exception for said certificate.
Great thought. There is another possibility due to the precise timeframe in which this happened, but the OP should try your suggestion first, then contact me by PM if it doesn't work.
I use AKO and what not just fine with a CAC reader and Norton 360 installed on my personal laptop. Not to say it didn't take some doing. You have to make sure all your software, drivers, reader firmware, and security certificates are up to date and integrated properly.
Its not an official military site, but I find it more helpful than anything else. It has step by step guides on how to setup your CAC to work properly, and all download links are to official sites.
I can't tell you how many times I have used this site to help out government employees to get their own stuff set up. It works.