It may be that the amp is still sending the signal to the PF and only disconnecting the return of the amp's loop when the loop is switched off. It could also be that the amp's loop is sending a "loud click" when it's being switched and this is being processed by the PF. Another possibility might be the cables you're using to connect the amp and the PF.
Does the PF do this when you bypass it using the PF switches (leaving the amp's loop active – as opposed to your OP where you're bypassing the amp's loop and leaving the PF active)?
If so and this happens regardless of how you bypass the PF, it may be a problem with the PF or the cables you're using to connect the amp and the PF. You might try using different cables.
If not, I'm inclined to think this is being caused by the amp's loop. Whether or not leaving the amp's loop active and using the PF switches for bypass is an option for you depends on whether your PF is accessible (on the floor) or not (in a rack or otherwise not under-foot). You might try contacting Earforce.