- Since Google switched to a secure(https) site the incoming keyword is not provided for text searches, are you looking at image data?
- Top pages will often have such a long list of keyword variations that even the best keyword for that page will only represent 10% of the total traffic, if that. Are you recording all keywords for a page and not just the best keyword?
- I've seen odd stats before(haven't we all) in which I would get spurts of traffic in 4 hour intervals for some pages/keywords and then go 4 hours getting it on others instead. It always seemed that I could predict x amount of traffic before the traffic would stop for any given keyword until the next 4 hour period began. I've stopped watching that closely unless a problem arises but this was just before Google switched to secure servers.
- Perhaps most importantly: Keyword research got a serious kick in the pants when Google started showing 95% of pages from one site only on top of any given serp. The reason being your TOP page will be ranked for a search based on the keyword but the rest of the pages Google shows may not even be ranked well for that keyword, they are simply related somehow, yet if a visitor likes the title on the 3rd page shown more it gets the click. In the past that never happened, the 3rd page (or 15th, 38th etc) would never appear for any given keyword because you had a better page.
Good luck getting accurate stats now with the sheer number of tag-along pages getting clicks on keywords they don't rank for, at least not well and never ahead of your better pages, but appear for with those pages.
example serps for keyword "widget", all from same domain
I search for widget, your best page is #1 but I like title in spot #4 more. Your stats pick up #4 as getting a click for that keyword but #4 would NEVER have been there forthat keyword were it not for page #1 and for Google's new way of showing many pages from one site. When you begin getting these multi-page results your stats are going to change.
ie: do you REALLY rank #1 for a keyword or are you ranking #1, #2, #3, #4, #5 etc and the 4th page is getting a higher CTR despite not being your best option for that keyword? Good luck tracking that, especially when your "extra" pages are shown only intermittently.