I expect you will hear back from Apple on this one.
I would expect this bizarre behavior from Motion 5.0.2 which was ... well... there are no words for what it was. I've seen my share of completely off the wall behavior. M5.0.5 has gotten much more stable.
Did you option-click-drag the link behaviors to duplicate them? Or duplicate them already populated? I've been burned so badly by 5.0.2 that to this day, if I'm working on a "real project" (not example stuff to work out forum discussion examples) I will "manually" create each and every parameter behavior from a menu and not use any available duplication method.
Save As the project to create a copy you can tear apart and reassemble. You should try to delete the layer with the ? and the Link Behavior that doesn't show up in the layers list (click on the linlk behavior's "title" line "Radius Link" in the Inspector and hit the delete key) Then re-add a new link and work it again [from a menu -- don't duplicate any of the other links already in use].
Looks like a very nice project. Hope you can fix it!