Omega theme conflicts with CSS of Seven administration theme, how to resolve?
When Drupal loads the Seven theme for admin, it doesn't load files from any other theme. Same goes vice-versa. So it's unlikely either theme can be to blame, or even involved.

There's no way to guess from here what styles are overwriting others unfortunately, you'll just need to dig further with dev tools until you find the culprit.

Methodically disabling contrib/custom modules and testing the results each time is a good idea if you can't see any where else to look in the dev tools, you can find or at least rule out a culprit that way. 

You could also search the files for those modules for instances of "views-ajax-popup", maybe something you have installed is specifically targeting it through CSS or javascript.