My script takes 0,5s to run without the debugger extension loaded. After enabling the extension and not yet debugging it takes 2,4s. When I debug/profile it takes 4,6s (the profiler show the total time 2s). I use lighttpd 1.4.15 with CGI PHP 5.2.3, PHPed 5.0.1.

Where is the problem?

does your script output a lot of errors/warnings/or notices? It may slowdown execution because debugger has to capture and store them all.
Regarding profiler, it's quite accurate and could not be that wrong. Check for example with function sleep or usleep (if you have it)