A co-worker lost CAC access to ONE of the DoD websites we routinely access. One, of the four or five we use on a regular basis. We tried switching browsers. We tried removing certificates. We tried re-installing (from our install file.)
In the end, it seems like following the instructions in this PDF did the trick.
Ultimately, I think the install-root file for the root certificate was newer than our file, and so I believe newer certificates were added. Also, the PDF mentioned some specific certificates that had to be removed.