Why have you set this up to reinitialize with EVERY update? That just seems like a an unneeded extra step.
AND, because the window prompting reinitialization trumps every other page of the dashboard, I can't even make a backup of the site (to backup my template.css file unless I go in by FTP! Ugh!
It would be great if you would more clearly state that we shouldn't be making edits to template.css-- that you would encourage a child-template.css to avoid being over-written!