I don't know if this is what you're seeing, but ...
1) Every search you do may end up being routed to a different data center, so it's very possible to see slightly different results within moments of two exact searches.
2) When Google finds two listings from the same site in the SERPs to be displayed, it grabs the second listing and moves it to an indented position right after the first listing.
That happens much more often when you set your display to 100 listings then when you're at 10, for example. Ergo ... it often appears as if the SERPs are different, when in reality all you're seeing is the clustering of results from the same site throughout your 100 listings.
Or maybe you're seeing something completely different. :)