The reason you have that funky library above QSYS is that someone did a
CRTDUPOBJ of SAVLIB and put it into that library. Then they probably ran
a CHGCMDDFT against that library. Maybe they changed it to save access
paths, or any number of other parameters. This is a very common practice.
It is not a bad practice. You are supposed to prompt the old and new and
see what defaults are different and write them down. Then you are
supposed to delete the old command, CRTDUPOBJ the new one from QSYS into
this library. Run the CHGCMDDFT again.
Object authority issues on the command are also a possibility.
I would seriously look at every object in this library.