WORK AROUND

The workaround/solution, if pending file rename entries exist for the jre installation directory after uninstall, is to reboot to cleanup the pending file rename operations.

P.S. lib\bundles\tnp\merged-rt.jar would be located under C:\Program Files\Java\jre6\ on XP.
                                     

SUGGESTED FIX

Parse PendingFileRenameOperations value from registry, to detect when an entry matches the installation directory and stopping installation or patch-in-place with "Error 25025.  A previous Java uninstallation was never completed.  You need to restart your computer before installing Java."

Added PendingFileRenameOperations to RegLocator.idt and AppSearch.idt so the registry entry is read and logged so we can tell the cause of the Error 25025 from a complete MSI log.

testcase: http://oklahoma.east.sun.com/deployment/www/tests/1.6.0_10/testcase_6681922.txt

webrev: http://sa.sfbay.sun.com/projects/deployment_data/6u10/6681922.0
                                     

SUGGESTED FIX

Read HKLM\SYSTEM\CurrentControlSet\Control\Session Manager, PendingFileRenameOperations, 
search data read for INSTALLDIR
If found, block install with a new error message.
Need to handle differences in case (C:\Progam Files\Java\jre6 and c:\program files\java\jre6) and shortnames vs longnames (C:\Progam Files\Java\jre6 and C:\PROGRA~1\JAVA\JRE6)
                                     

EVALUATION

removed "part of JRE completion process." from the synopsis since it does not require kernel to occur.
                                     

EVALUATION

Kernel performs the rt.jar replacement in two steps:

1) Delete lib/rt.jar
2) Move lib/bundles/tmp/merged-rt.jar to lib/rt.jar

So if the Kernel completion got interrupted or otherwise didn't complete properly, you could potentially see a missing lib/rt.jar but a still-present lib/bundles/tmp/merged-rt.jar.  The next JVM startup would then immediately attempt completion again (because the lib/bundles/tmp/finished file still exists).

But the symptom you're seeing, of a missing lib/bundles plus a missing lib/rt.jar, doesn't make sense for Kerneel.  Removing lib/bundles is the very last thing Kernel does.  It would only remove lib/bundles if the rt.jar file had been successfully moved into place, and it would never remove lib/rt.jar after having already removed lib/bundles, since the trigger conditions are then gone.

Chris suggested a plausble explanation for this: an uninstall notes some files being in use and marks them as delete-on-restart.  You then continue to interact with the computer normally, installing a new Kernel JRE and so forth, without realizing the lurking danger.  But when you eventually reboot the machine, the delete-on-restart time bomb goes off and lib/rt.jar is deleted, destroying your JRE.  This explanation seems far more likely than it having to do with Kernel completion, especially since you specifically said it only happens after a reboot (reboots mean nothing to Kernel; it neither looks for them nor acts specially upon them).

Reassigning to install team.
                                     

EVALUATION

This has likely been the behavior in all releases of Java.

The fix should be to check the PendingFileRename key prior to installing, to make sure that files aren't going to get deleted after a reboot.