site: search algo broken or different?

Why are pages ranked differently?

[Kabby]

If you do a search for: widget

Then do a search for: widget site:.com

Obviously there are non .com sites in the normal search results, but the .com sites/pages are in a different sequence in the site:.com search to the normal search.

Why are they not in the same sequence?

What clues does this give on the algo?