Very strange. It looks at first glance as though you had knowingly or unknowingly reset the notification area icons
If so, they should have repopulated as you opened your favorite programs that show up in the system tray notification area.
But from what you are saying it appears to NOT be doing that or they would have shown up before now.
And it seems to be hitting more areas than that as it doesn't let your administrator account do what it should by rights be able to do.
This could mean a bunged upgrade to 8.1 or having an infected computer with more than your average adware/PUP/malware.
Over time since the upgrade to 8.1, have these icons reappeared and then gone again at times?
Did the upgrade to 8.1 appear to hang, did you have to reboot in the middle of it, etc. Anything odd during the upgrade?
Are you using a very invasive cleaner program that is set to reset the notification area icons every time it is run?
Just some things to think about until jcgriff2 or one of the others can pop in with more helpful hints.