Yes, Apache execute it as nobody. Maybe because it isn't ascribe to any VH - it's only a ScriptAlias. Forcing group nobody (at cPanel server) isn't good idea, because Apache/Lsws execute as nobody, so there is now way to set permissions safely.
The logs are cleaning after processing, so I can't help you now in this way. I may only disable cleaning logs and wait for next mistake in counting bandwidth.