If you've read this post and gotten a little lost as to the struggle he (Tony Bibbs) faced to lead up to, you might want to check out the previous post outlining all of the things he came across when making the move from Zend Studio version 5.1 up to version 5.5.
So what have I concluded out of all of this? As clearly as I can state it here is the big problem. With Zend Studio 5.1 you could install Studio Server with no additional fee outside of the Zend Studio license. This allows you to debug via your local Apache instance running PHP. To get the same feature set out of Zend Studio 5.5 you would have to buy Zend Platform separate.
My hunch is the folks at Zend expect developers to debug on their local desktops with only the internal debugger which *can* produce different behavior than that under your web server environment. It's not good if your debugger can exhibit different behavior than your web server. I should also note that remote debugging with Zend Studio 5.1 while serviceable was not the most stable. It would occasionally kill Apache, possibly require me to restart Zend Studio or rare cases even force me to reboot.
He also lists out some of the other issues he's noticed in making the change (six of them).