regular serps vs advanced search

what is the difference between the regular site search and advanced search

[RobinK]

Huge difference in number of results when doing more from this site and then going to advanced search and searching the domain (the site has a unique name that is on every page so it should be the same I would think).

When doing the advanced search there are 3 times as many pages from the site that show up then when I just search for say widgets.com and click more results from this site.

Anyone know why the pages would only show up on advanced search? The site recently had quite a few url changes that were 301'd, would this have anything to do with it?

[RobinK]

anyone know, is this the sign of a penalty or could it just be the url changes and 301 issue?