Mike,
I’m sorry I missed your last message. I cannot think of anything that would be causing this mess up, I used your web.xml file to see if there was an issue with parsing it, but it worked out fine. Is this a maven project by any chance? If so, please send me the pom.xml file.
Would it be possible for you to send us a smaller version of your project, something which is sufficient to replicate the issue? If so, please email it to support@genuitec.com ATTN Brian.