Having multiple Xalan libraries is a common source of problems.  Check either
during the installation, during the first load of Lenya, or during every load of
Lenya (recommended if process is fast).  Pseudocode would be something like:

classpath = Get CLASSPATH;
pathList = Parse classpath;
For every path in pathList: XalanList = GetFiles({path} + {OS Directory
Separator} + "xalan*.jar")
(XalanList should be structure XalanVersion = XalanPath, so each version appears
once.  HashMap?)
If XalanList.length = 0:
   Message "No Xalan found.  Lenya will not work."
Else If XalanList.length > 1:
   Message "There are more than one version of Xalan.  This causes problems with
Lenya.  These versions were found:"
   Message XalanList values for paths (one per line).
Else (XalanList.length = 1):
   If Xalan is at least minimum for this version of Lenya:
      Message "Using xalan-{version).  This is good."
   Else
       Message "Using xalan-{version}.  Lenya may have problems.  Please upgrade
Xalan to at least xalan-{requiredVersion}."
   End If
End If