Problem solved. It's such a simple little thing to. When I installed the update when the problem first appeared I wiped my WoT cache and reset my settings. As a result, the gun sights defaulted. I did not have the armor pen enabled in the gun sights...
I'll repeat: I did not have the armor pen enabled in the gun sights.
Armor Penetration marker is now working.
Thanks for all your help Aslain. Sorry for being a dork.