Today, Tony Bibbs provides something that "Zend might not want you to know" about using their debugger in your application - that it enables an option silently, without asking the user at all.
A co-worker here was going through similar problems with Zend Studio 5.5. He'd even gotten so frustrated he tried installing phpEclipse and in doing that installed Zend's debugger. Little did he know that by doing that he had enabled remote debugging support in Zend Studio 5.5 without the need for Zend Platform and we can still happily use APC.
Now the million dollar question is why doesn't Zend document or promote this fact? Sure, they want you to install and test drive their "PHP Application Server" but if you don't desire all of that why force it down our throat?
He points out a PDF that only barely mentions that this could happen but couldn't find much else. If you don't want this to happen to you, he provided a different method to enable the debugging easily through a few php.ini settings.