I am having this exact same issue and have tried fiddling with switch 48 and then going to the switch test menu and seeing if it's closing by pushing the ball past it on the rail behind the ring and it is (with the playfield down). Then when I get to the last shot on DTR it still doesn't register.
A post above mentions it 'Just sucks my first experience with DTR was in test mode' - does anyone know how i could test this without actually getting to the last shot on DTR to see if the DTR show will activate - obviously if this is possible it would save a lot of time!
Cheers