Good deal! It looks to me like is was the chmod, which makes since since php.cgi runs under suexec and the directory needs to be 755 on DH.
That said, the changes should be immediate - but again what browsers cache locally remains a mystery to me, and seems to differ greatly depending upon the browser as well as the circumstances. Possibly just the reload of the page triggered the execution of the php.cgi with the new permissions?
Hey, at some point, once you've figured out what works, the rest of the mystery become a bit academic.
If you do ever figure out why it behaved like that, I'd appreciate you sharing!