Seeing a few new updates out that I wanted, I just ran the updater. I had Blender, jPortable and LibreOffice to update. Blender updated fine but jPortable gave me some grief.
First, the install was not silent (if this is due to needing to accept the EULA again, ignore this as an issue), but after accepting the agreement, it gives the default install location as "_online.paf.exeCommonFiles/Java".
I then cancelled the installation of it (I wanted to run the updater again to verify that it wasn't a one-off issue). It continued installing LO as it should have, but reported jPortable as being installed correctly.
On second attempt to update, it updated correctly and silently (I'm guessing because I had previously accepted the EULA?).
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This was fixed a few minutes before you posted with 7 Update 4.1. It was an issue with CommonFiles plugins using PA.c Installer 3.0.2, which has been updated to 3.0.3 with the fix.
Sometimes, the impossible can become possible, if you're awesome!
You must have pushed the files through between my first and second attempts to update as my version is at 4.1.
I just wanted to get in quick before too many people had downloaded, but obviously you were on to it as well.
The updater thinking the install was successful when I cancelled it is still an issue, although minor in the scheme of things.