Of course yes, a bit.
If Google has a cache with the all 'old' urls, and now you submit the new url's setting (eg. with a sitemap), this is the result.
It doesn't mean that this depends from Sef Advance, but from the new architecture that google needs time to crawl, accept and takes as definitive url. You need time to have a great result. But really great.
In addition Sef Advance will hold 'alive' the all backlinks if some site still point to a content of your old style url.
From FAQ, the main things I've followed are:
configure your Sef Advance (without enabling any cache)
be sure that the setting works and is valid checking components and so on.
enable cache
Tags like alt and h1 are very important, even if maybe in some case you have to hack your template.css
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