Now i have just to find out why this happens

You could try strace (facetiously aka "Almut's Golden Hammer" at the place I work... — yes, I do tend to slightly overuse it, but it has definitely helped me numerous times to solve problems within minutes, that other people before had messed around with for hours or days ;)

This might help to debug how/if the query string is handled apache-internally, and where exactly the error occurs that leads to it being dropped. At least if the problem is replicable enough that you won't have to wait thousands of requests for it to occur. To ease debugging, you might want to start up apache in single process mode (option -X). Also, don't forget to trace forked processes (the CGI script) as well (option -f).