If that doesn't... Then I would rename ~/.config/i3/config
And after that maybe .bash_profile or .bashrc or .bashRename them to something else, if the problem continues then you can change the name back to the original.
In an extreme case I would rename all ~./config to something like ~/.config_old
The only thing I can't think of is that something in bash or in config is executing something you don't want, that is why root works but user doesn't.
Of course this only if /home is decrypted
