I have two Apache servers running PHP. One accepts forward-slashes in the query string and passes it along to PHP in the expected way, for example:
http://server
http://server/index.php?url=http://foo.bar is not a valid url. You have to encode the slashes. I think browsers do this automagically, so maybe you were testing with different browsers?
http://server/index.php?url=http://foo.bar
Or perhaps it's the AllowEncodedSlashes setting?