I don't know the answer to the problem exactly--but .NET has a very similar problem.
If you look at the .NET-versioned WSDL Readme.txt, you can see that it has an issue at runtime. The resolution for .NET is the following (I don't know if it maps to what to the java code but maybe it'll give you a pointer).
From readme:
Resolving Errors which Manifest During JIT
With the current code, one can compile and attempt to instantiate the AXLAPIService class. However, one error will manifest as the types are inspected and loaded.
- Class XUserUserGroup has a field which was generated incorrectly. One must remove one of the ?[]? from the two ?[][]? brackets after XUserUserGroupUserRolesUserRole field:
public XUserUserGroupUserRolesUserRole[] userRoles;
