Ok, lets try to limit the problem area.

Phex is not touching anything that has something to do with file permissions and also Java has no way of manipulating file permissions for user/group/all separately. Thats why I would look into the direction of a bug in Java, its platform specific implementation or in the platform installation.
Additionally some change between Phex build 89 and build 92 must have caused this bug to appear. Phex changed file handling from using streams to none blocking IO which could be the cause...

I searched a few times through the Java bug database but without finding anything usefull...

Lets look at what Phex is doing...

Phex stores your sharedlibrary into a file called sharedlibrary.xml.tmp and then after its finished it copies the file to sharedlibrary.xml.

As I can see on your screenshot the problem must happen during the copy operation since the sharedlibrary.xml.tmp is still with correct permissions. So what has changed between 89 and 92 with the copy operation... a few lines have changed but unfortunalty it still works the same way as before and most important it still uses the old file stream handling.

So after all I'm stuck again...

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