File Upload Url

Well it seems that I have another hurdle and this one seems simple enough. But a dozen Google searches have put me back where I started.

I have a multisite setup and the main blog urls are written as /blog.dir/#/files... and the images show up as expected. When I create a new blog to use as a template with New Blog Templates plugin the urls I get are written like this.. /sitename/files/...

The files are being uploaded to the correct place spot /blog.dir/#/files but since the image urls show up in the front-end as /sitename/files/... I'm not seeing the images.

More info: I'm running WP 3.1.2 and the main site is not rewriting the url it's using blogs.dir/#/files... and that's working for me. But the 2nd site and all templates based off of it are uploading the images but displaying the wrong url. When I edit the fileupload url manually the in the settings I still get the same /sitename/files/... which leads me to believe the urls are getting re-written somewhere. in the process.

Has anyone experienced this before? Is there a way to disable that front-end rewrite?
just need some ideas.