What you hear is perfectly explainable and it's all about "Phase Cancellation".
I don't often double a guitar part by using the same guitar. If the problem is that you have two takes of the two performances of a guitar part played on the same guitar, it's going to be very difficult to separate those two. The guitar parts will just sound very similar and the overtones of the part will tend to superimpose on each other.
In that situation, I would have suggested using a different guitar for the second part. If you only have one guitar then it may be possible to play the same but using different chord shapes. By using inversions of the chords and different positions on the neck, you utilize different strings for different notes, which automatically solves that phase cancelation that you have now.
If that's not possible, it may be possible to detune the guitar for the second take by a semitone and then put a capo on the first fret. Again, you are using different parts of the guitar, different strings, different hand positions and therefore different fundamental pitches of the native strings to play the same part but in a manner that will cause the overtones of the two parts to be different, which also solves your problem entirely.
I hope this helps.