We have two versions of our site, one with frames and one without (for crawler friendliness). On the first look, they look very similar, but the frames version (with 6 frames) is much more feature-rich. As desired, the no-frame version does turn up in Google searches, and I have a JavaScript pop-up dialog on these pages which asks the users whether they want to be redirected to a 'frames' version. The frames version of the page has "<NOINDEX, NOFOLLOW>" meta tag, so it is not crawled.
Would the presence of such a script affect SERPs? Our original content is very relevant and we have high page ranks, but we have much lower SERPs than other sites with lower Page Ranks and lower relevancy.
