What other mods have you installed??? Perhps something you've installed has modified a core file in a way which is causing the issue you are having.. Either that or something went wrong when you applied the modifications needed for the core file edits required for Super Orders OR Super Orders is installed incorrectly.. The fact that this started after installing Super Orders is merely a coincidence I'm sure..
I suggest either try applying all the Super Order file changes again, and if that doesn't solve the issue for you, you should try rolling back to a pre-Super Orders version of your store.. Test to see if you still have the e-mail issue, if you do then try re-installing Super Orders again..
The Super Orders install is straight forward, and there's no reason this should be happening unless you've installed something incorrectly.. (and I don't know what since I cannot re-create this issue at all in my test store..)