That section is actually a recreation of a synth part from the original track. I agree it sounds kinda weird, and that's why I painstakingly matched the original to within a few milliseconds. As far as I can tell, its originally recorded in free time, because there seems to be no internal logic to the timing and rhythm.
I do agree that it sounds awkward; which is a problem in the mixing, i think. Now that I've been able to step back from the track for a while, I hear a lot of things I could have done better in the mix, and not having that part so much in the forefront is a big one. Pulling it back in the balance, adding some reverb/delay to reduce the abruptness of it; I had quad tracked the guitars, so maybe taking it back to two for that section, etc.
As for the disparity you hear between the two of them, I don't know what to tell you. There isn't any difference: I copy pasted those guitar parts, because it took so much work to get it right four times, I didn't feel like doing it again for four more.