Issue with DocType Entities. XALAN/Tomcat 6 or what?

We use JDOM 1.1 to transform raw XML into HTML snippets.

I recently upgraded to Tomcat 6.0 on OS-X and have noticed the following warnings in the logs:

[Deprecated] Xalan: org.apache.xalan.processor.TransformerFactoryImpl
[Error] admin.xsl:6:80: Document root element "xsl:stylesheet", must match DOCTYPE root "stylesheet".
[Error] admin.xsl:6:80: Element type "xsl:stylesheet" must be declared.
[Error] admin.xsl:7:26: Element type "xsl:template" must be declared.
[Error] admin.xsl:8:19: Element type "html" must be declared.
[Error] admin.xsl:9:10: Element type "head" must be declared.
[Error] admin.xsl:10:12: Element type "title" must be declared.
[Error] admin.xsl:11:79: Element type "link" must be declared.
[Error] admin.xsl:12:78: Element type "link" must be declared.
[Error] admin.xsl:14:10: Element type "body" must be declared.
[Error] admin.xsl:16:31: Element type "div" must be declared.
[Error] admin.xsl:17:41: Element type "div" must be declared
...

This annoyance is triggered by the use of entity declarations like:

<?xml version="1.0"?>
<!DOCTYPE stylesheet [
      <!ENTITY pound "&#163;" >
      <!ENTITY nbsp "&#160;" >
]>

I have tried various configurations of XML APIs in my Tomcat6/lib directory but all seem to produce the same results. Currently I am running the following from the XALAN 2.7.1 release: xalan.jar, xercesImpl.jar and xml-apis.jar.

Any clues?

Nick