While I don't know what is causing your problem, in the future, you need only run the latest combo updater. In your instance, you didn't need to run the 10.3.5 before running 10.3.6 combo.
I would apply the 10.3.6 combo updater again, and try a different account, if you have one to see if the same problems exist. If they do, that indicates a system problem, if not, it is a user specific problem.