How should I file an issue on drupal.org that affects multiple modules? I have an issue that is caused only when three modules are enabled together (logintoboggan, pathauto, and entity).  When I upgrade entity from rc1 to rc3, one of the functions of logintoboggan breaks if pathauto is enabled.  I have attempted to determine which module is interfering with logintoboggan, or if it in fact is logintoboggan itself that is at fault, but this exceeds my debugging ability.

So, in cases where one has an issue where a specific combination of modules causes an error, where should the issue be filed?  Should only one issue be filed, or should multiple issues be filed and linked to one another?
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.