Ultimately this problem was caused by an error that has been fixed. The system I am loading into uses the library JAXB-2.0 where I thought I was using the latest version (JAXB-2.2.5). Thanks to a poorly designed plugin framework, my version was being pre-empted by the 2.0 jar.
In order to get past this I'll have to either upgrade the library of the commercial software, or try and play with Classloaders
Thanks to everyone who helped me to find this.