Bad config file - it probably has incorrect settings for data directory. As to why, not a clue. Probably something got screwed up during installation, which is most likely due to that 'repack' thing you're using.
What's usually a good fix: deinstall all that bloated package junk, remove all MySQL services that are installed already, reboot, then get a standalone MySQL server instead (free from
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). These days it comes with a decent GUI installer too, so it shouldn't be too hard to figure out.