This morning I woke up, looked at my phone and saw there's another Superuser app in my app drawer. This is the one by ChainSDD that has the pirate logo. I rooted via the method on DroidRZR forums and that gave me the Superuser with the white "#" logo by Clockworkmod. There is no option to uninstall ChainSDD Superuser, it doesn't even appear in Titanium Backup Pro or Clean Master. I can only uninstall the "#", but doing that made my phone think it was unrooted (reinstalling the "#" Superuser fixed that).
Yesterday I flashed the deodexed and 1% battery mods (no icon changes). I also flashed the CM10.1 ROM and GAPPS on ROM Slot 1. However, I did not notice the new Superuser immediately after, and I am pretty sure I wiped my ROM slot yesterday (did it again just now, ChainSDD Superuser is still there).
I'm not incredibly concerned about this, I don't think it's a major issue, but it is weird that the ChainSDD Superuser just appeared on my phone and can't be uninstalled and I'd like to figure out what might have caused this.