This is an odd one and perhaps another clue to the penalty mess.
Once upon a time, I enjoyed wonderful rankings for a whole bunch of terms. Then the penalties started. Well, we all know that tune and it's a sad one. Up and down, but mostly down, in a big big way.
Now here's the weird thing:
Google's Webmaster Tools/Query Stats page shows a #14 Top Query Search Clicks ranking with a #3 Average Top Position for one of my important two keyword phrases. Yet when I click the phrase (or otherwise run a normal query) the phrase does not appear on the Google search results page.
I also have a very important one word phrase that's in the same boat - it shows at #6 and #7 on that Webmaster Tools chart, but is nowhere to be found in the search results.
My site is clean, all original content, been around for a decade. No doubt I've made a mistake (or mistakes) somewhere along the way, but trying to figure out exactly what is making the algos angry is making me crazy (and driving me to the poor house).