Re: The requested URL /groups/ was not found on this server.
Sadly statements like this make me wary:
I really am not 100% sure.. I just was sopse to be the designer… I paid a developer back in May and he still hasnt finished it and wont contact me… (awesome!)
Christina you do not need to be adding in index.php to your permalink paths , you have a fundamental issue elsewhere and I think it lies in a how your site really is structured and a lack of understanding therein.
Set your permalinks to a normal structure remove all the custom stuff. You have an apache server and unless there is something screwy with mod_rewrite or a failure to write to the .htaccess file then all should work as expected.
Can you tell us where BP is installed to, as at the moment the top level index page of that site makes no sense to me, and all your links appear as page_id=
