You are outside the box, by changing tons of stuff. People who operate inside the box won't be able to help you.
And it is even less likely when you are dishonest in the original email. You claimed your sysupgrade use was completely normal, but it isn't. It is far from normal. When we get reports like this where people "touch the insides", both Florian and I regret that sysupgrade ever arrived in the system. We want to delete sysupgrade. Or, every month or so change the internals so that it will delete some people's machines. Does sysupgrade recommend what you do? No. But you do it. Do you understand the concept of "you own all the pieces"?