I think you are right: this looks to be a problem in ardour or jack.
Yes, i did. I'm trying to record 2 mono tracks: voice and guitar.
In ardour i have 2 tracks that i imported and 2 new tracks i added and armed for recording.
In the ardour mixer window i assigned to these new tracks the input: system:capture_1 in one track and system:capture_2 in the other.
In jack i checked the connections and everything seems to be ok (for what i can understand).
Capture_1 connects to audio1/in1
Capture_2 connects to audio2/in1
Audio1/out1 connects to master/in1 (Audio1/out2 to master/in2)
master/out 1 and 2 connect to playback_1 and _2.
At my eyes everything is well connected, but i guess it is not so.