For the past few months, I've been pulling the GA Queries report for every Monday, to get a birds-eye view of several different metrics, including average position. Now, I know average position doesn't mean the highest position a page is found out for a keyword, but an average of all the impressions for a keyword in a given time period. I get that, but it's currently one of the best ways to do what I want, and the trends are still pretty telling.
All seemed to be well (other than the discrepancy in numbers between it and Webmaster Tools' version) until the last month or so. Suddenly the GA report is showing a lot more keywords from page 5 and higher that have crazy amounts of impressions. However, they're short-tail, high-search keywords, so I figure they might get more impressions than your average keyword. I did note that these keywords don't seem to show up in the WMT report, and thought that was a little weird.
Then I saw something today that took the cake. Our brand keyword was being reported at as being on the third page. Panicking a little I looked it up, only to see that it was at position 1 today as it should be. The GA report also showed it on page 6 on Tuesday. So I went to WMT, and wouldn't you know, position 1 for every day this week the data was available. And that other keyword? Still not showing up.
Am I wrong to be using the GA data? Should I switch to WMT instead? I like GA because it has all the click data, but if GA is going to give me bad data, I'll use it instead and just make up a number for the >10 clicks.