I have this happened ever time i upgrade Pro Sites Setting disappeared a day later after upgrade.
Yes you have heard correctly all setting are just cone.
I will then put them back and then hit the save button and they are all fix till the next upgrade.
Guys i wish there is more info on this to help you guys get to the bottom of this but there are not .
If and body had this same problem please post here so we can get to the bottom of this