Ok I fixed it.
The problem was with the WAR directory, when you first create a mockservice you give it a path for the war directory and all of the .jar files are copied to it, the next time you rebuilt that war file it pulls the .jar files from this path and not from the SOAPUI internal location, it only updates .jar files that are new or are changed, .jar files which are not present in soapui but are present in the war directory are simply copied into the war file. This means that when you update SOAPUI the old versions .jar's will be present and retained unless you delete the WAR directory and rebuild it from scratch.
From a user perspective the problem here is that there is no indication what the problem is and no suggestion that you might need to delete the old war directory and since rebuilding a mockservice war file following a soapui upgrade is likely to be a fairly infrequent task it is likely that this will always result in a fair amount of troubleshooting before the user remembers the issue.
One solution that might work is to give the user an option on the Deploy Project as War dialog to overwrite the war directory rather than update it when they select a war directory path that already exists.
