That explains it then. I see how this happened now. It was already fixed in the ZIP earlier today.
In this case it is safe to manually change 4.0.9 Beta 1 in the setting to 4.0.9
Since the installer uses multiple upgrade scripts based on different configurations, the wrong version list was used to set the version number. For example, when MySQL is at least version 5.6.4, an additional set of upgrade scripts is used which makes optimizations for newer MySQL versions. The last version in this branch was 4.0.9 Beta 1. The setting took this value instead of the value from the main branch.