How should I file an issue on drupal.org that affects multiple modules?

Question

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?