This issue might be related to having more than one Steam account.
The Portal 2 config should be located in [SteamPath]\userdata\[UserId]\620\remote\cfg\config.cfg.
[UserId] consists of random looking numbers. If there is more than one such folder, the optimizer only uses the first one to get to the config. So that might be something worth to check.
Deleting the folders that weren’t my own profile did it, thanks :D