My vote goes to the hammer. Sounds like something is dragging the hammer when it gets into a certain position or something with the trigger. Because the odd shot is almost always about 5" low and the rest of the shots are so consistent, that odd shot must be coming out slow. I have the same airgun...Gen 2 Synrod, LW barrel, all still stock. I haven't seen anything like your problem, I just get a good tune with great groups and then they seem to start opening up and I can't figure out why. But I searched the forums and wound up polishing the hammer and tube it slides in with 2000 grit abrasive sheet to reduce friction. Then I coated the tube with a teflon spray that dries out and leaves no residue that can cause gumming up or collecting dust. Also polished the trigger parts. My other problem with opening group sizes was solved just last week. I broke the gun down (not any pressure parts) and decided to try more trigger pull. I think it was too light so I increased it somewhat, even gave it a little bit of creep and my groups size is right back where it was, 1/4 to 3/8" at 25 yds. Let us know what you find out.
Barry