Interestingly enough I am getting that same error. Maybe there is a step that is intuitive to you that is not on the website (or the more likely scenario, I am misreading something). However this is the process that I am following:
1. Download the Full DB from the website
2. Load it into SQL with HeidiSQL
3. Download the Repository and run the merge_windows.bat
4. Load the resulting SQL file into world with HeidiSQL
5. Launch worldserver.exe
6. Watch it crash out and remember I have to change the field name in the command table from security to permission
7. Re-Launch worldserver.exe
8. Watch it crash with the aforementioned error: "[1054] Unknown column 'quest_repeatable_rate' in 'field list'"
HeidiSQL does tell me that there were two warnings from my query but I see no way to find out what those were.