I think there might be a bug in Server 2012 installation of software through GP.
I have a GPO that includes different software that I apply to all PC, ie: chrome, firefox, flash.
I removed flash from the GPO and I have it setup to uninstall the program when it falls out of scope. After I did that, both chrome and firefox disappeared from the settings tab but still appear when you edit the GPO. I did a gpupdate on a PC and it uninstalled all 3 programs even though I only removed Flash. I selected redeploy for Chrome and Firefox and Chrome now show up in the settings tab. I did gpupdate again and both programs reinstalled.
Can anyone reproduce this?