I found a solution in case anyone finds this question in the future.
The issue was that I had previously obtained jars from an installation of old websphere 6.1:
- bootstrap.jar
- classloader.jar
- emf.jar
- ffdc.jar
- j2ee.jar
- ras.jar
- wccm_base.jar
- webserverices.jar
- wsdl4j.jar
- wsexception.jar
These jars had been passed to me via unknown other other, with no version numbers or metadata of any form. I have no idea if they are real releases of intact, but they work. Initially I was using them with the provided websphere 6.1 JRE (java 1.5), but as I was now deploying to websphere 7.0 I changed my software to use the websphere 7.0 (java 1.6). What I wasn't aware of is that the jar's and the java 1.5 release were specific to each other, so when using the java 1.6 JRE the Emitter class wouldn't fail, simply generate an incorrect wsdl.
To fix this, I just changed the software back to use the java 1.5 JRE until I have the time to correct the jar's.