Sort of curious about this statement because starting wow from the bnet launcher or starting it from the wow executable should result in the same process getting run in the exact same way,
At some past point you chose to run one as “Run As Administrator”. This would result in a different windows account getting used to launch wow and that could result in the permissions getting changed on the WTF folder or the files in it.
What specific methods are you using to launch wow? How are they different?