Problems running Cocoon 2.1.5 on Websphere 5.1

[will . durrant]

I'm having problems running Cocoon 2.1.5 on Websphere 5.1. The first problem is that I can't build cocoon with my java_home set to point at IBM's jdk. I can get round this by using sun's jdk but I'm not sure if trying to run it using a different jdk than that which it was compiled, is a bad mistake?
The built war file successfully deploys to Websphere but upon running many of the samples I get either:
- ResourceNotFound exception : org.apache.cocoon.ResourceNotFoundException: No pipeline matched request: welcome

Or for other samples I get _javascript_ related exceptions such as :
- org.mozilla._javascript_._javascript_Exception: java.lang.UnsupportedOperationException: getWidget(id) got deprecated from the API.
- Error 500: org.mozilla._javascript_.NativeJavaPackage: method <init>(Ljava/lang/String;Ljava/lang/ClassLoader;)V not found

Any help or advice much appreciated,

Will