Almost certainly your site template CSS. I think every instance I've ever seen of popups appearing in the wrong place were down to CSS issues. Which can be solved with an override, either in yur Fabrik template custom CSS, or at the site template level using J!'s override mechanism.
Inspect it with something like Firebug, and check to see if the template is applying any kind of offsets on the .modal class.
Typically with anything to do with positioning or layouts, it'll be CSS related. So the best thing to do is give us a link to the page, so we can inspect it directly.
-- hugh