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Most often Java installs don't finish correctly due to Java being in use at the time of patch installation. You might want to perform a pre-installation reboot of systems or look into writing a script that will close down any software that might be using Java prior to performing patch installation.
We have been seeing the same issue - any installation of java 7.0 below patch 40, it will attempt to install then remove the whole application, all servers with versions above this appear to be unaffected by this issue all versions below version 7 are not affected. we have raised this with support.