Hi guys, it's probably too late to reply. But I was having the same problem, and what I did was to cancel from the "Pending Procedures" tab -for the agent with the problem-, the one named "Start KLC on (name of the agent). After that I was able to connect with out problems.
Interesting... We are having this issue with one user. And as far as we can tell it is his account on his machine that is coming up with that message. In order to work around it after logging into the portal and starting the live connect session, the VSA address is placed in the browser address box again and navigated to (hit enter key). Then it comes up. If we log into his machine there is no issue with live connect. He can log onto other machines and also has no issues. Thought at first it was a Kaseya update issue (6.2), then thought it was a MS patch issue. Now we're stuck. We stumbled upon the workaround but would really like to fix it for real.