I dont't know exactly how to solve your problem.
I think basically it's a bug or problem with two instances of compass running at the same time on the same folder.
But due to your environment, I have a suggestion that can do the trick for you.
Why, instead of having two folders with the assets, one for prod. and dev., you just keep one, for both dev. and prod.
What you can set on compass is to output css in the way you want for dev. and then pass that css through a yui filter (or whatever) for prod. This will minify all assets. If you are using symfony, you can use assetics, for instance.
That's the way we do and works perfect. We don't use assetics for compass... that's another topic :D
If you don't use any framework or extra filters, you can alway manually dump the assets when this ones are ready for production.
This way you avoid using two compass instances at the same time and also to compile manually for every deploy on production.
I really think it have to do with having two instances of compass running.