This seems to be a common problem when PHP is running in CGI mode (e.g. check http://issues.ez.no/3693 )
You have two options:
- get rid of the first question mark, which seems to done by setting EZ up in virtual host mode (not sure as I've never had this problem) - get rid of the second question mark by always using post instead of get
If only the search functionality causes this problem I just would change the form from get to post. As far as I know you don't need to change any kernel code as the content/search.php uses the function hasVariable() which does check both post and get (I hope).
If you are really using php in cgi, I'd suggest to find a provider that either provide mod_php or fastcgi (needs some tuning on the server, but works fine). It will run quicker.