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The rebooting was just a side note, the real problem is the two missing files.
Just for the heck of it I modified the transform to set Reboot = suppress and for good measure also RebootYesNo = no
Not only does this not resolve the issue of the two missing files, the system still reboots after installing from an AD deployment!
I've noticed that some machines I test this on will have the charsets.jar but are still missing rt.jar
This leads me to believe that the machine simply reboots too quickly not allowing the unzipcore custom action to complete leaving one or both of the largest files unextracted.
Interestingly, core.zip is deleted prior to rebooting.
Which brings up two good questions:
Why doesn't unzipcore complete? It's set to execute synchronously in the install sequence!
Why does the system still reboot at all?
I have a feeling that if I introduce a custom action after unzipcore that simply pauses for 10 seconds everything will work out, but this seems like an unnecessary hack.
Turns out this is a similar situation to what I was encountering with JRE 6 u12 in this post
Unlike that time, no pop-up windpw was being generated in the unattended installation, but the installation was still stalling due to iGateway.exe.
GREAT JOB SUN - you "fixed" the pop bug up by simply aborting the install, fantastic! [sarcasm]
I created a new transform which stops and starts iGateway as per the previous case and this resolved the installation, now JRE 6 u18 installs successfully with ALL the files needed.
How you brought back a bug that was fixed four releases ago I have no idea.