Previously using Linux, switched back to Windows, the problem was not occurring when using Linux, guitar recording only panned to the left
Are you trying to record in stereo or mono? If you are using a normal mono microphone set both Windows and Audacity to mono. (A true-mono file will play through both speakers.)
If you are recording in stereo, set both to stereo.
I set both windows and audacity to mono and it works now, thank you.