I have looked at your site and imported a few pages, it seems that the pages that are derived from the template are having some linking issues. I'm curious about the steps you took to get it this way. By default all of the links should be generated automatically for you based on the structure specified in the wizard. Is this not the case for you? If you had the site generated with the bad links please explain a little about the steps that you took to create the site like this so we can check into this.
It looks like a few of your links just have a company/ in them that is causing them to break, is this something that you have added in after the fact to account for something else? Please post back with this info and I will try to help determine what may be going wrong.