I know this exact problem you describe, and I am almost 100% positive it is not the fault of a mod. This is because my duo, using standard official composite cables, exhibits the exact same problem. The reason I never noticed before is because I never played my duo on anything but a crt until last year. Not only the duo, but snes, genesis, sega master, they ALL do it to some degree, some more noticeable than others. The reason we never noticed it via composite in years past, is because we were all playing on crt's(or up to some point were).
It varies from crt to crt even, with my rgb modded tg-16 on a small crt completely unnoticeable, on a large crt, just barely noticeable, on a large lcd, more noticeable, lcd via composite noticeable, lcd stretched via composite, very noticeable. lcd stretched via component, well you get the idea...
I think it is a flaw of the design in these old systems that was overlooked, as you would probably never notice it on composite, or even s-video, or component on a 27" or less crt tv.
There is another very similiar problem atari 7800's exhibit when s-video modded due to the two separate luma(or chroma lines i can't remember) signals conflicting. Keep in mind crt's have a tendency to smear or blur edges and such faint lines would be completely unnoticeable on most crts via composite or even rgb. Also many people doing rgb mods on the old systems have reported the faint vertical lines. I think the reason some people notice it over others, is that usually no two people that have an rgb or component modded system have the exact same display setup, also differing degree's of vision, and peoples ability to distinguish fine details (on my rgb mod, my friend didn't even notice the vertical lines, until i pointed them out.) I believe there are things you could do to lessen the problem, but the fact is that the lines are a result of the systems design, not the parts used for the mod.
If only I had a dime for every person with a rgb modded system who has the lines...
