I added a custom field that is configured for one project and a subset of the available issue types.

I attempted to add this custom field as a comment in the issue navigator using Issue Navigator > Configure. The field shows up in the "add columns" selection and when I add it, it shows up in the designer tool. I can move the column to where I want it. But when I view the issue navigator (i.e. not in configure mode) the column is not there. I changed the assignment of the custom field to "all issue types" and the problem went away. This bug appears similar to 5933 but not exactly the same.

A possibly related problem is that the custom field does not show up as a filter choice in the Filter>New or Filter>Edit screens. When I change the application of the custom field to "all issue types" then it does show up in the filter construction screens. The custom field is a radio button field and it is configured to have radio button search.