Have you ever tried to access the Wall Joins tool where you have only two walls meeting? Such as in a T intersection scenario like this:
On my Revit 2014 system, the Wall Join modifiers will not activate in the Options bar when clicking on the above join.
However, if you add a bit of temporary wall, like this:
You can now access the Options for the Wall Join. Set your option, then delete the temporary wall.
This workaround allows you to set the “Don’t Clean Join” option on a 2 wall T-intersection…
Another tip – if you have trouble selecting a particular Wall Join, select two or three walls that participate in the join and then use the sunglasses to Temporary Isolate Elements. You should now be able to select the proper join.