Does the over-locknut (OLD) of your rear wheel match the spacing of your frame? Sounds like it does not. When putting a track wheelset (usually spaced to 120mm) on a road frame (usually 126mm or 130mm) it is necessary to add the appropriate amount of spacers on each side of the wheel, so you don't have to crank the axle nuts way down and bend the frame every time you install your rear wheel. This isn't totally necessary, but makes things a LOT easier to work with.

Regarding chainline, did you actually measure it or are you just eyeballing it? I can't eyeball because my eyes lie to me. When it's wrong it looks straight and sometimes vice versa. Usually the little ring of a double will match up with the hub. If not, there's no issue re-dishing the wheel a bit unless you want to use it as a flip-flop.