It's been a very long and frustrating waiting game! Now we can finally start to test upgrading from php 5.4.x to php 5.5.x! Here is a quote from their forum: http://forum.ioncube.com/viewtopic.php?t=4109
Version 4.5 loader packages are now available from our Loaders Page (http://www.ioncube.com/loaders.php) and include loaders for PHP 5.5.
As previously mentioned, the PHP 5.5 loaders will run PHP 5.3 and PHP 5.4 encoded files and are available for Unix-style platforms such as Linux, OS X and FreeBSD. Windows loaders will follow in due course.
Loaders uploaded to files1. Please allow 24 hours for rsync to other mirrors.
CustomBuild 2.0 also updated to allow the install (it previously blocked php 5.5 for installing it)
The CustomBuild 1.2 code didn't appear to block it previously.