BuddyPress.org

As ive read thru the codex i see theres two ways of doing the permalinks depending on your server. mine seems to have defaulted to the pathinfo version of permalinks which automatically has to place index.php before the permalink for it to work. because of this the BP links are thrown out of sync as their links do not recognise having index.php thrown in front of their link. any ideas how we can work round this?