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I looked at the code and the column alignment is stored in the metadata.db file in the library. You can see the saved alignment by looking at the metadata_db_prefs_backup.json file in your library, searching for "column_alignment". The information is saved in both the metadata.db and the .json file when calibre exits. The .json file is a backup.
If Aerofs is overwriting your metadata.db then you might be in a world of hurt. I suggest that you run check library to be sure that books you have added are really in the db.
An easy test: start calibre, change the alignment for tags, and quit calibre. Look at the .json file to see if the alignment is changed. Note that a column is listed only if its alignment is not "left". If the alignment is "left" then start calibre. If it becomes "center" then something, such as a plugin, is changing it at startup.
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