If the guide rod was the cause of the scraping, you would see similar score marks on the part of the rod that contacted the frame.
If the guide rod is truly mil spec, then one thing that could cause this problem is if the rod either wasn't assembled into the slide correctly, with the curved part against the bottom of the barrel, or it somehow rotated during the shooting cycle.
Your comment about the Brown rod suggests to me that that is the problem, and that it is either at the maximum tolerance limit for mil spec, or it isn't really mil spec. Either way, you might try to get a mil surplus rod, and see what happens.
H4444, if the slide is binding, then there will be some scoring of metal somewhere. In your case it will be subtle and hard to find, but if you persevere, you will find it. That done, you can then diagnose and fix the problem.
Good luck, guys.