Okay, I found the problem. A step was added to the Lite upgrade in the wrong position at some point (I think it was RC 2). The position of this step changed the offset of the update-the-addon-version step, which is supposed to be the last step to run. However, it looks like it was running before nearly every important step in the upgrade process, which caused the following steps to be skipped (it's already on the next version number, so why run the steps for the last version).
If your wiki is still empty, the simplest remedy for this would be simply to uninstall and reinstall. Please let me know if you have any problems doing this. I can't be sure if all the missing data will have an effect on the uninstall process.
Since it was a problem with the upgrade script, I am marking this issue as fixed and committing the fixed upgrade script to the Members area now so no one else runs into this issue.