Recently my account got banned. Admittedly, I ran the bot 24hrs on that account so it didn't suprise me.

What surprised me is that I started another account and never launched the bot again, but got another ban after a few days. Then I remember that each time I started the bot after a few recent updates of the game, the bot said it patched something and asked me to restart the game.

Now I can't help thinking that the bot may had put something detectable into the game client itself.

If you started a new account with the same mail address, or same name, or same payment method, it is linked to the previously banned account.
In case any similar suspicios activitiy is then detected, you will be banned again, since your account is already flagged due to aforementioned primary ban.