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FYI,
Since I too have experienced this change (in the past), I thought it might be helpful to post the clip and bat file I use for Saxon 6.5.5 jars.

Below is the info,
Have fun,
Mike Ferrando
IT Specialist
Library of Congress
Washington, DC
(202) 707-4454

*OS: Windows XP
*Folder Structure:
workshop
  |__batch
         |__saxon655.bat
  |__documents
         |__my.ead.finding.aid.xml
         |__my.ead.finding.aid.html (transformation output)
  |__errors
         |__error.txt
  |__shared
         |__char_ent (dtd stuff)
         |__ead (dtd stuff)
         |__styles
                |__my.awesome.stylesheet.xsl

*Clip (with Line Numbers):
1  ^!Set %drivex%= ^$GetDosOutput(ECHO %CD:~0,2%)$
2  ^!Set %drive%=^$StrTrim(^%drivex%)$
3  ^!Append %drive%=\myworld
4
5  ^!Set %directory%=^?{Document directory=_^%directory%|documents};%docname%=^?{XML document name=^%docname%};%xslname%=^?{Style name=^%xslname%}
6 
7  ^!Set %xmlfile%=^?{XML file=^%docname%.xml};%xslfile%=^?{XSL file=^%xslname%.xsl};%htmlfile%=^?{HTML file=^%docname%.html}
8  
9  ^!CLOSE ^%drive%\workshop\^%directory%\^%docname%.html DISCARD
10 
11 :^!Info ^%drive%\workshop\^%directory%\^%docname%.html
12 
13 ^!dos ^%drive%\workshop\batch\saxon655.bat ^%directory% ^%htmlfile% ^%xmlfile% ^%xslfile% "replace=^%xslname%"
14 
15 ^!WAIT
16 
17 ^!open ^%drive%\workshop\^%directory%\^%htmlfile%

================
*Comments:
Line 1,2 find the drive letter and assign the var to "drive"
Line 3 appends the home folder to the drive letter 
Line 11 is commented out, but will gives the trace variables from the clip if you want to see them in an alert window. (remove the ";" to actuate)
The clip displays a window with fields for stylesheet and xml document.
Don't put the extensions in the fields.
Just the file names.
The output always has ".html", but it is really whatever you have transformed it with.

*Batch File: (workshop/batch/saxon655.bat)
@ECHO off
SET CLASSPATH=.;c:\saxon6.5.5\saxon.jar;c:\saxon6.5.5\saxon-jdom.jar;c:\saxon\saxon6.5.5\saxon-xml-apis.jar
java -Xmx500M com.icl.saxon.StyleSheet -l -w0 -o ..\%1\%2 ..\%1\%3 ..\shared\styles\%4 %5
PAUSE



----- Original Message ----
From: Michele R Combs <[log in to unmask]>
To: [log in to unmask]
Sent: Wednesday, October 22, 2008 4:41:30 PM
Subject: Re: Saxon question

Saxon question  
Well,
as I discovered only a couple of weeks ago, thanks to this very list (check the
archives for helpful details from several people!) you can switch to Saxon
6.5.5 and then you wonąt need that pesky virtual machine at all, which is
what we ended up doing.
 
Michele
 
 
From:Encoded Archival
Description List [mailto:[log in to unmask]] On Behalf Of Lill, Jonathan
Sent: Wednesday, October 22, 2008 4:06 PM
To: [log in to unmask]
Subject: Saxon question
Unable
to start the application. The Microsoft virtual machine cannot be found. 
Class not
registered 
Jonathan Lill 
Project Archivist 
The Museum of Modern Art Archives 
212.333.6514 
[log in to unmask]