There might be incompatibilities between encoded files generated by latest zendenc53 and PHP 5.3.2 - or older zendenc53 generated files and PHP 5.3.3 and above.
Please install Zend Server and try the encoded application again.
If you cannot install Zend Server for any reason (will replace distro PHP on the target server),
you can try backported PHP5 packages from a higher Ubuntu distro PPA (see the following question for example):http://askubuntu.com/questions/77468/ho ... -mysql-5-5
The most supported stack for Zend encoded applications is Zend Server, which includes PHP 5.3.9 in the latest version 5.6.
If you need sample PHP 5.3 encoded scripts for testing, send me a PM.