It seems to happen more if I have JRiver in a paused state rather than a stopped state when installing the upgrade. If using update channels, I can cancel, restart JRiver, press CTRL + J, and then let JRiver download the update again. It always works on the second try.
I do have library server running and if I close JRiver and then shut down the Media Center process before manually running the update file I have much better success.
Rebooting always fixes the issue for that installation, but is a hassle. I can work around rebooting.