3.1 permalink for Custom tag – /index.php/index.php/

I have read a lot here about permalink problems with 3.1 and had a similar experience to many people it seems. I have a Custom permalink structure /index.php/%year%/%postname%/ Initially links to a custom tag I use as an A-Z in http://www.dorchesterchamber.co.uk gave me 404’s so I move back to 3.0.5 and have loaded a test site http://www.whitebears.co.uk to do some testing. I have managed to get it working by playing with the permalinks BUT now when I look at the url for a selected tag I see an extra /index.php/ I am nervous about updating my live site to 3.1 until I can find an explanation/fix for this. Any ideas?