Hi, I've implemented the handling og the "with_front" parameter in the Rewrite section of register_post_type() API call.
My code allows you to not use the default permalink schema. In my example I have setted permalinks to "/post/%postname%", but you'll get something like /post/POSTTYPE/postname) but NOT the more SEO compilant link like /POSTTYPE/postname.
With my edits this is now possible. I can't post the full new code or my edits here... feel free to download and test it from my blog post here: http://thepanz.netsons.org/post/wp3-custom-post-types-and-permalinks