This is an issue which has been around since at least V6, but I would LOVE to see fixed in an upcoming update.
If you duplicate an Instrument Channel, the original channel gets bussed to Output 2 (if you have more than 1 Output enabled). The new copy goes to Output 1, as it should.
This happens to me daily, and has done on every project for the past year or so.
Hope someone can confirm this, and that it can be added for a future update.