Ed Finkler points out (in his latest blog entry) a problem he's noticed when using Zend Studio 5.5 related to its default path.
In the php.ini file used by the PHP5 executable, the include path is hosed. If you installed in the default location and are running Windows, you'll probably find the file at: C:Program FilesZendZendStudio-5.5.0binphp5php.ini
The problem is that the value of include_path isn't wrapped in quotes, making portions of it act like a comment and "hose" your directory path. Thankfully, it's a pretty simple fix - just quote the value and be on your merry way. It's one of those bugs that has the potential to be so small that it'd be very frustrating to find.