I'm unable to make ioncube encoder work with Apache 2.4.12 and PHP 5.5.8. So, this is what I've done by now:
1. Installed httpd-2.4.12-win32-VC11 [http://www.apachelounge.com/download/]
2. Installed php-5.5.8-Win32-VC11-x64.zip [http://windows.php.net/downloads/releases/archives/]
Their raw combination works ok - I can run php scripts etc. I then:
3. Installed ioncube for Windows VC11 (64 bits) [https://www.ioncube.com/loaders.php]
I made corrections to php.ini and when I do php -m I see that it loads ioncube extension without any errors. However, when I now start Apache I get an error with a message about zend_get_hash_value and php5ts.dll. (PS. Combination with Apache 2.2, PHP 5.4 and ioncube works for me, but it seems rather outdated).
It seems like you have mismatched the thread-safe version of Apache and the ionCube Loader. PHP extensions have to match exactly the version that they run on, that is PHP with thread-safety enabled has to have a thread-safe Loader.
To confirm this, go to the output of your phpinfo(); and look for the entry Thread Safety. If it says disabled, make sure you have the Non-TS version of the ionCube Loader (Win x64 Non-TS zip). Likewise, if it says enabled, make sure you have to thread-safe version of the Loader (Win x64 TS zip).
Furthermore, please consider using 32bit PHP / Apache on Windows, as PHP 64bit is still marked as experimental and can cause issues with the ionCube Loader:
The x64 builds of PHP for Windows should be considered experimental, and do not yet provide 64-bit integer or large file support (source)