When I saw the title of this thread, I thought of one solution to this issue (but not with Di2) and that's to look at the cable clamp.

If it's turned 90 degrees (installed wrong) the tab goes into the parallelogram on some models and prevents it from closing all the way.

Just thought I'd drop this in in case someone googles for a solution to this problem and ends up here.

One other thought, and that is bend metal last. Read manuals first. I'd be surprised if torquing on the hanger was necessary.