One developer noticed the differences and posted a question in the forums asking:
I'm using the Google Webmaster Tools API to get data about our site's keywords (in Google's eyes).
But something's strange- the keywords showing up in the API feed are not quite the same as what's showing up when we used the web-based tool.
Has anybody else noticed this difference in the data?
I know that the web-based data is quite a few days behind, so one theory I have is that the API data is fresher. Just guessing at this point.
This is not uncommon being that the data is refreshed often and data filters can play a role in the results. But also, sometimes, APIs access slightly different data sources and can throw the numbers off. Finally, Webmaster Tools is known to have reporting bugs often - so that can play a factor also.
Or maybe, this was just a random fluke? Do you have this as an issue also?
Forum discussion at Google Webmaster Help.