If I search for 'widgets', my site is #4. If I search for 'what are widgets', my site is #3, even though Google says "what" and "are" were ignored due to being very common. I can replace "what are" with any combination of ignored words, even the Spanish ignored word "en", and my site is still #3. What's going on?
I've noticed this too when search for "shopping for widgets" google says the for is ignored, but "shopping widgets" is totally different results! Maybe this will be fixed when the backlinks are gradually added ;)
One of the things the algorithm assesses is the location of words on the page. Things can be weighted a bit differently if the main words in the query are directly next to each other or separated by something. A common word might be ignored for content purposes, but it would still have an effect on the location and spacing of other words. This likely accounts for the ranking variations that you're seeing.