Are you supposed to copy the folder to run multiple instances? I was actually running 4 (all different sites) at once from the same folder, even with the same exe name. I didn't do anything special -- just launched the same app 4 times with no issues.
It's not necessarily required, but it is recommended. Otherwise all 4 instances of the bot try to read/write to the same DB file and this could and does cause issues sometimes. It doesn't always, but it could.