WMT ranking data and possible penalty - is position "raw" or filtered?

[FranticFish]

I'm seeing something unusual on a site and wondered if anyone had seen something similar.

One of the site's main terms (two words, non-geographic) seemed to be hit in mid-December, and rankings dropped immediately about 9 pages.

As far as checking ranks in Google by searching (logged out, in browsers that are never used to surf or click results) is concerned, it has recovered about 4-5 pages. However:

(a) WMT ranking data says it has more or less COMPLETELY recovered; and
(b) the site still gets lots of referrals on long-tail phrases that include this main term - in fact, most months, more than ever.

This is the first thing I've seen that smells like a penalty on a site in years so I'd welcome other recent experiences, specifically:

1) Does WMT data differ from 'real' data?
I'm wondering if WMT is showing what the ranking would be were the site not filtered for that term.

2) Do specific keyword penalties affect only that term and not variants of that term i.e. 'green widget' is affected but 'big green widget' is not?

[ZydoSEO]

1) My experience has been that the ranking data in WMT is misleading. It takes into account all URLs on your site that might have been shown for that same keyword phrase as well as all of the positions it might have been show at. If you drill down by clicking on the keyword phrase in WMT and compare the Search Query screen rankings to the keyword phrases URL/position data, you'll see what I mean.

2)Yes. Google has had the capability for a long time to filter or penalize a particular URL for a specific keyword phrase, while variations of the phrase might be unaffected.

[FranticFish]

Thanks for the input. I've always used Analytics rather than WMT but I've just compared the slightly different systems on short periods of 48 hours. They are pretty much in agreement - BUT what they agree on is far better than what I've been seeing, and normally when I check ranks manually they are slightly better than the data from Google.

Re: 1) In WMT it is always one url shown for the phrase no matter where it ranks, so it's not different urls being amalgamated. However the business has a strong Google Places listing in a major city on the key phrase which has been unaffected throughout.

Does Google fold local data (i.e. the A-G maps listings) into the WMT/Analytics rankings reports?

[FranticFish]

Answering my own question: it appears they do. I have a site that has been rock steady at marker 'B' in a major city for its key term for years and that is consistently shown as '2' in Analytics and WMT.