I took some time to look into this and found the problem. At least on my system, all files in the jdk folder are assigned to the correct user, but the files in jmonkeyplatform/jdk/jre/bin are missing the executable permission bit.
In the case of the broken update, jmonkeyplatform tries to use jmonkeyplatform/jdk/jre/bin/unpack200 to upack the downloaded files but fails since it does not have permission to run the executable.
Running “chmod +x *” inside jmonkeyplatform/jdk/jre/bin fixes the issue.