While trying to solve the problem I had in this thread...
http://forum.cockos.com/showthread.php?t=136390
...I unearthed a bug with "Input channel name aliasing/remapping".
When it's checked, the signal on audio input 1 appears at both channels 1 & 2, while the signal on audio input 2 disappears - no audio.
Unchecked, the audio inputs work fine.
I had renamed my 4 inputs to:
mic/line 1
mic/line 2
MOX L
MOX R
Using "Input channel name aliasing/remapping" makes it impossible to create stereo recordings from "mic/line 1 + mic/line 2", and for mono recordings I lose an input - mic/line 2.
All inputs are fine when "Input channel name aliasing/remapping" is unchecked, but then I lose the names.
I'm using a Yamaha MOX 6 with up-to-date drivers, and I'd like to stress that it works perfectly with Cubase & Studio One on the same system.
This must be a bug in REAPER.