From Drake's answer..
"you will then see a drop down window menu. Select what you want to record in the channel. (ie Right voice, Left voice")
This is really important. When you select a record channel, it defaults to listening to one of e.g, R1, R2, multipad 4 etc. So if you are playing your flute part on voice R1, you must make sure the record channel is listening to R1.