Even if you weren't those courses might have been created with an experimental version of WW that created fields for "flags". I think you can just ignore the error -- the extra field for those courses won't hurt anything. When ww2.5.2 is ready for prime time those upgrade errors will go away.
I'm not sure about the visible flag but I think that won't cause serious errors either. All that might go wrong is that some homework sets that used to be visible will have the visibility box unchecked and the visibility checkbox has to be checked again.
The comparison between what's in the database and what ww22.214.171.124 is expecting can be fixed by doctoring the databases for the old courses -- I think you'll find they have extra fields for flags and visible that the current courses don't have. -- but it's probably not worth the effort of fixing these tables by hand.