Are you SURE this is what's happening? I seem to remember that one of the parameters (autodosbox?) can cause two instances of the program to start running.
While we're on the topic of "are you SURE this is what's happening?"...

For the past few weeks, with increasing frequency, when I would load ZSNES games from Mamewah, sometimes I'd hear the windows "DING!" immediately, and ZSNES would load but not respond to any keys, and the only option was Task Manager to kill off ZSNES, then everything would be normal. Load the same game again and it'd be fine. It was MADDENING, I tell you.
Then I started noticing (sometimes) the same "DING!" with Mame stuff, only it wouldn't lock up -- just an annoying ding. I tell you, I was THIS CLOSE (missing visual) to reinstalling my OS out of desperation.
Then I discovered Shuffleshot. Shuffleshot's game selection uses the 1 player start button through all screens. Sometimes it would work fine, and sometimes it would mysteriously skip an entire screen.
The next "DING!" was inside my head. My microswitch for my 1 player start button was going bad. Rated at 100,000 presses, my behind. If it was the FIRE button I'd say "sure, it got that many presses in 3 years, if not more". But 100,000 presses of my 1 player start? I don't believe it for a second.
Anyway. Obviously this is not what's likely happening to mosesmalone. I only mention it because (a) I think it's funny and (b) it's an example of a problem with game starts looking like one thing, but being something else entirely.
Che