I'm not familiar with your amp, but does it have send and/or return level controls? If so, you should be able to adjust these to compensate.

The PF by itself shouldn't cause a huge drop in volume. Version 3 beta 16 of the software includes an output level control to help compensate for small volume differences. If you haven't, I'd try upgrading your pedal to the latest software and seeing if you can adjust the output level to compensate.

http://eventide.com/Home/Eventide/AudioDivision/Products/StompBoxes/PitchFactorUpdate.aspx

Does your amp do this with other pedals in the loop? How much of a volume drop are you experiencing? 3db? 6db? 10db? More?

Do you get the same volume drop if the PF is set to DSP or DSP+FX bypass as you do when it's set to RELAY bypass (PF UM p43)?