For the audio, the only way an iPad would have access to individual channels on your PA would be if the PA advertises more that one Bluetooth input, and you connected to the wrong one. I've never heard of a device that does this, but I think it's possible. Normally an audio receiver would just have one destination that the iPad can see, so if the audio is coming out of the wrong PA channel, it's a problem with the PA itself. You said you were using an audio cable instead of Bluetooth, but the same rule would apply -- unless the mixer has multiple inputs and you physically connected your cable to the wrong one, this can't be a problem with apps on the iPad.
For the layouts, were you using your iPad in a different orientation (portrait or landscape) than normal? Layouts are matched to the screen size and orientation, so the list will change when you rotate your device. That's the only reason I can think of for layouts to disappear and reappear again.