You were very thourough, though you cannot connect the tiny cubes directly to the receiver unless you have the ability to set a 150Hz or higher x-over. The crossover for the cubes is in the bass module, which is why they are hooked to it.
The definition of a passive sub is that it does not have it's own power, so if you don't plug it into an outlet, it is passive.
Does that card have a digital out? You would do much better to use that than the bastardized version of analog you are currently using, and the problem you describe would seem to be directly related; are the output for the sub and center on the same cable?