I spotted an interesting Google Webmaster Help thread where a webmaster was asking why the most used words on his site is not showing up in the keywords report in Google Webmaster Tools. It seems like, at least for this report, Google may consider certain usage of a keyword to be over usage and would consider those keywords either boiler plate text or common words.
Jonathan Simon of Google said in that thread, and let me quote:
The Keywords list will sometimes exclude words that we determine to be boiler plate text or common words. This varies from site to site. The Keywords list is a starting point to see how Google is interpreting your site's content. This list should be evaluated in tandem with what's listed in the Top Search Queries report for your site as well as how your site appears in the actual search results for the keywords you're targeting.
He goes on to explain that although it may not show up in the report, due to possible Google issues, this should not impact the site in a negative way. He said:
Boiler plate and commons words (excluded from the Keywords list) vary from site to site. It sounds like for your site we could be doing a better job here.
The more important question though is if this negatively impacts your site's ranking as you mention. It doesn't. That's why I said the Keywords list is a good starting point and that it should be considered in conjunction with other information.
The question I have, is this not helping your site? I guess not.
Forum discussion at Google Webmaster Help.