Try each of the following steps in order until the issue is resolved :
  1. On the Course record mark the marking column as graded for the appropriate academic year. 
  2. Log in as a supervisor in Faculty Access for the Web and grant view/edit rights to the marking column.
  3. If the marking column is still not visible in Gradebook, Clear the Server Cache.

If teachers have already accessed the marking columns then report that they come and go:

One organization that hosts their own data on-site reports that restarting the EE server then restarting the FAWeb server did clear the issue.