It's easy enough to determine the cause of the problem using a simple "divide and conquer" routine. I'm guessing the problem is in the amp and the easiest way to determine that is the swap the L&R input at the amp. So now the interconnect from your pre-amps Left channel will connect to the amps right channel input and vice-versa. If the problem remains with the right channels output from the amp, you now know the problem is either the amp or speaker cable on the right channel (since you already tried different speakers, right?) or possibly the power conditioner. You could also now try swapping the L&R speaker cables at the amp end to see if the problem moves to the left speaker. (The problem will obviously move if it is the amp).
You can also try simplifying your system to a minimum configuration just to insure that there are no other influences on it. I would guess that you could remove the interconnects from the amps inputs, plug the amp directly into the wall with no pre-amp/source attached and see if the speakers driver is still pumping.
If you still have the problem with just the amp and speakers (no input components or power conditioners installed), then you pretty much know it's a problem with the amp. If the problem (driver pumping with no source attached) goes away in the minimum configuration, start adding components one at a time. I would first recommend connecting the pre-amp only before plugging the unit back into the power conditioner.
If you get confused about the process of elimination, draw yourself a block diagram of the system and cables. As you "swap" things, make note of what you've done, or X out any component that has been identified as working properly. You'll quickly get to the source of the problem (I'm guessing it's the amp or power conditioner based on your original comments).