(I’m answering this old post because no one else did and I hope it can help the user.)
Given that the problem goes away once you remove the effect of the built-in pedal upon volume, it sounds very much as though (i) said pedal is not working properly, or just maybe more simply (ii) you have it parked at 0, a.k.a. angled as far towards the ceiling as possible, or maybe (iii) if it is at 100%, a.k.a. as far forward as possible, you have inverted its Min and Max settings to 100% and 0% in the Vol block.
So, as the simplest option, check whether moving the pedal with it set to control volume has any effect.
If not, try testing/calibrating the pedal as described at the bottom of this page: http://line6.com/sup...?st=0#comment_0
If that does nothing either, there are various past discussions about possible mechanical/electrical issues with the pedal and how to test/fix them on this forum, the old archives, and possibly other sites; you could check whether any of the posts therein solve your problem.
If you are still unsure, post back, and probably there are other users here who have experienced this first-hand and/or have links to old threads discussing it.