If you mean power on the system, see that there is an update, download it, delete the old directory, unpack the new directory, run the game, then I have always made clean installs. I don't play one version and then see if there is a new version and unpack/play that without rebooting.
Is there something outside of the install directory I should delete?
I'm not technically knowledgeble enough to know what the cause is here. None of the previous builds I ran had this issue. :(