How should I file an issue on drupal.org that affects multiple modules?
Personally, I would pick the one with the highest level (or least mature), and post in that issue queue.  By highest level, I mean the one closest to the user, the one with the modules dependent on it, etc.  In your case, I think logintoboggan would be most appropriate.

Then in the issue, explain the situation in detail and mention the other modules.

If the project owner thinks a lower level module is the culprit, then they will decide what to do.  More than likely, they will post a comment, and reassign to a new queue.

I would not post the issue in multiple queues, though.  It makes tracking things too hard.