The config file is reset whenever the client launches.

I couldn't find anything in the logs that would explain it.

Are you making the changes in the file itself or in the Config GUI in-game?

The file itself. I'll change this to false. After I start up the game, it will be back to true.
Show the 'Press Control for more Info'-Text on Item Tooltips
B:"Advanced Info Tooltips"=true

Try using the in-game config option and see if the bug still occurs.

I can't reproduce, neither with the GUI nor the file directly.

Actually, never mind.
I can reproduce.
This is very odd.

I didn't want to waste your time or anything. But this has slowly been driving me mad.

I edited the config with the gui in game and then hopped intoa single player world and the config change stuck (no tooltip). I'm restarting the game now to see if the edit stays.

Yeah, after restarting the client, the config is back to normal.(meaning that line is set to true)