None of these things should be happening, or at least no one has ever reported behavior like this. I've been issuing it for areally long time and never see anything remotely like what you're reporting. You should also not need to manually kill Xpadder, it closes cleanly after the emulator closes unless you have a setting wrong or there's some weird permission issue.
The enumeration counts the number of connected controllers and launches profiles based on that. It doesn't work for everyone though, so it's hit or miss.
I don't understand the part about the batch file, the plugin does all this internally abs you shouldn't need to do that. But based on the other behavior you're describing, I think you have deeper issues.
Can you post your configuration file?