I've seen responses to this issue via Google but those responses were inaccurate based upon my experience.  My studio setup is pretty static.  Signal routing and sources remain the same project-to-project.  Like many of my other projects where this issue is not present, I have two guitar tracks recorded direct from my Line 6 Helix via the stereo SPDIF port.  Again, this is how I do all my electric guitar tracks.  For the project in question, Pan doesn't do anything on these two tracks.  The track remains panned to center.  I even attempted to place Channel Tools in the tracks but it does nothing as well.  Nor does placing a mono FX last in the signal chain, routing to a bus, converting the track to mono... Nothing will pan these two tracks.  I used the same setup to do other projects and they pan exactly as you would expect:  more or less signal to the L/R channels as you move the Pan pot.  Anyone have any idea how to fix this?  Can't build a mix with the guitars panned to the center.
 

Can you post a screenshot of the tracks and the console?  I don't know whats going on but here are some things to try.
- Make sure you are not in offset mode
- If you import or drag in a wave file to another track can you pan that one?
- Are the tracks stereo or mono? You said you used the Stereo SPDIF so is each track stereo or are they recorded to two mono tracks?
- Have you tried the interleave button to see if that makes a difference?
- Is the Helix your output device or are you using a different interface?
 
Just some Ideas.

I'm not at my DAW but I think another trick is to use Bounce to track and create mono tracks from the stereo ones. 
And with my SPDIF I can choose left or right or stereo so you can always see if that is possible and only record to mono. 
 

A screenshot is worth a thousand words

I'll get a screenshot when I'm home from work.  The Helix feeds the SPDIF input of my RME AI and T-Bolt to the PC.  It is a stereo track.  I have tried interleave.  I have converted to mono.  I'll try copying the track to a new track.  But as I've said, I have other projects recorded the exact same way with the same equipment and same configuration and am not having this problem.  Also, not in offset mode.  The two guitar tracks are both stereo and were recorded separately... as I have done with most of my other projects.
 

https://imgur.com/94fwaPO
 
screenshot fwiw
and copying the wave file to a new track won't pan either.
 
However, if I open one of the wav files in Audacity it pans normally  Feels like a Sonar glitch.
 
 

Your master bus's interleave is set to mono.

bitflipper you are THE man.  Thanks so much.  This was driving me nuts.  Thanks again.
 

Like Jonesey said, a picture says a thousand words.