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jre-6-windows-i586.exe /s IEXPLORER=1 MOZILLA=1 REBOOT=Suppress
I was able to stop the Automatic Updates from occuring by setting a Software Restriction Policy using Group Policy. I blocked the JUSCHED.EXE and JUCHECK.EXE files from running. When doing a manual check, a couple of errors are logged in the Application log, but the user sees nothing. Should work the same for a scheduled check.
As of 4-18-07: Downloading from "jre-6u1-windows-i586-p-s.exe" http://www.java.com/en/download/manual.jsp does not work. The installer is apparently missing its transform. Download from http://java.sun.com/javase/downloads/index.jsp instead. This package is not distributed with the silencer.
At the moment it looks like it's not possible to globally disable automatic updates. JRE 6.0u1 doesn't recognize the EnableAutoUpdateCheck or JavaUpdate keys. Instead the information is stored in binary format in HKCU\Software\JavaSoft\Java Update\Policy\EnableAutoUpdateCheck, and that information does not carry over to other users, even if the NTUSER.DAT file is copied over to the default user. JRE 5.0u6 is the most recent version where the automatic update behavior can be controlled for all users.
Here I published a tutorial for it and many others programs. Please comment on the blog if you have questions.
I have built ZEN deployments for several versions by extracting just the MSI and building an MST using the property settings listed in this section. In previous versions, the MSI was self-contained. Today I found that the msi for v1.6.0_23 no longer has the files compiled with it so the data.cab file also has to be present for the distribution.