What are the 2 amps you are using?
I have never ran multiple amps together before, but from I have seen and heard on here, a common problem is phase issues with some amps when they are run together. If i remember correctly from reading on here, the phase issues will cause the low end of the amps to disappear and the mids and high end to sound strange, which sounds close to what you were saying about the wah. Generally speaking, out of phase issues cause certain frequencies to cancel out and certain ones as a result to become more pronounced.
http://www.tonebone.com/re-bigshot-aby-detail.htm
The pedal you have has ground lift (which I never recommend using at all, which can electrocute you if ingaged).
It also has a phase switch (this is the one with 180' under it) and an isolation transformer ( marked "iso"). Just for fun I would turn on the "180'" switch real quick to see if the problem is fixed and it may be just as simple as that. Doing this wont damage anything, it either will fix the problem or wont fix the problem so there is no risk.