When EQ is installed in a directory where it doesnt have write permissions (i.e. Program Files) then it writes files to the AppData directory. If you did something to correct this which allowed EQ to write to its own folder that would likely be the cause (Wouldnt think just changing the compatibility mode would do this)
Did you move the EQ folder outside of Program Files or maybe select the box to run the program as admin? Either way, good to have it working like this for the future. Makes it far easier to find files like logs/screenshots/char files/config files etc
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