I would install 2.0.6 the link I gave you before should take you there. One of the previous vs (don't remember which one) had a security vulnerabliliy.

If you follow the instructions that are in 2.0.6 you shouldn't have any problems, unless something doesn't transfer ftp properly. If you have a log on your ftp make sure you have it turned on when you are ftping, so if errors come later, you can check what didn't get uploaded