AfterBurner has to be running after the reboot. Did you set it to run at startup? Just look and see if your overclock settings are still there in AfterBurner after the reboot. If not, I guess you didn't save them.
If I open up Afterburner, I don't see any options for my cards. The 4 GPU Cards show up but everything is greyed out and I can't change any settings.
Please Clarify, from your first post you've done overclocking, so now its now greyed out?
but when I start the rig up I don't think they are overclocked anymore
There is an option in MSI afterburner to start the App in startup, what you need to do is to save first your Overclocking setting by clicking the floppy disk Icons and tick the windows startup option.
So when I was overclocking originally, I did it one card at a time and it worked fine. Now, when I have all 4 cards connected, it is greyed out and I can't change anything.
I did one card at a time, and all my Hynix cards worked fine but the Elpida one would crash on me.