Hi Chas
I might be way off here, but I noticed on your screenshot that the two guitar tracks both contain stereo waves.
From experience, I've sometimes experienced some panning weirdness when I've accidentally recorded stereo audio tracks instead of mono.
Did you record the two tracks in stereo deliberately - in other words, is there different information on each channel?
If you accidentally recorded in stereo instead of mono, try bouncing the two tracks down to mono and see if that solves the problem.