Definitely the scopes, the rails line up with the original gun-sights themselves.
I guess parallax problems do occur because when I shoulder it, the reticule changes from "zeroed" to "not-zeroed" depending on the mounting. Sometimes I mount it, discover it works fine, then stare down the sight again to discover it's "off". Already tried an extra rail set, I use a larger mount for the sight to see over a PEQ box. Even with accounting for both, the sight is still off-centre.