Can you help me with permalinks it Multisite?

Hi I am having an issue with a new Multi Site install. I have had a blog for a while at Today we made it multisite but a couple of things are happening.

1. I can change permalinks for the default site so they dont have index.php

2. my site has not been moved to gareths and does not include this in the link

3. Everything seems to work fine for subsites. e,g

Is this a config issue or a rewrite issue? Unfortunatly life is not so simple for me as my server is on nginx. Can you please help?