I think this is because your xampp has php compiled as module and godaddy probably has php as cgi.
For the seo thing, some search spiders, some of them diesn't read anything after the ?. maybe google reads it but other could not. i'm not a seo expert at all, but you can read about in seo forums.
Anyway, i think you can avoid that index.php and index.php? from your url. just take a look at http://ez.no/doc/ez_publish/technical_manual/4_0/installation/virtual_host_setup or do some search about "avoiding index.php" in this forum.
At least Google will index URLs with question mark. Though there might be some issues with complex URLs with parameters. But in this case there shouldn't be any problems with indexing. Although clean URLs are of course nicer.
More info about this in Google Webmaster Center http://www.google.com/support/webmasters/bin/topic.py?topic=8522