I am having the same problem... I just upgraded to 12.1.3 from 12.1.1101.401 using the auto upgrade by dropping the new sylink into the current server. The server upgraded fine, but now they are all showing offline for the past 14 hours.
They are current on the virus definitions, but the will not connect to the SEPM. I have cycled services on the client machine as well as my SEPM. Policy Profile Update was done as well with no change. I have SEVERAL more servers that I need to this upgrade and having them show offline is not good.