There is absolutely nothing wrong with equipment being in between the speakers. 99.9% of systems are setup this way. Of course, ideally, the speakers should be farther out in the room than the rack the equipment is on.
I suspect, as others have said, you have an isolation problem, or a mismatch betweem arm and cart.
I suspect, as others have said, you have an isolation problem, or a mismatch betweem arm and cart.