Ok, so I'm doing some testing again. This is what I've gathered:
It appears that the speaker lines or something may be crossed somewhere internally.
If I plug in speaker 2, all of speaker 1 activation points work on speaker 2, but not on speaker 1.
If I plug in speaker 1, all of speaker 2 activation points work on speaker 1 but not speaker 2.
The PA works the only with speaker 2 connected, not speaker 1.
All the auxiliary tones, Ecto1, Bad boys, etc work on either output, either speaker no matter how is configured.
Hopefully that makes sense to everyone. So it works, its just backwards. Strange.