Re: Manual wah before or after compressor?
Is it a wah with a boost? If so, maybe put it before the compressor, so the compressor knocks the volume down a little. Personally (I know it's a little backwards) but I like the compressor after the amp's input and/or overdrive. Then it's more like a studio effect applied to a raw amp sound, rather than artificial compression before the preamp.
So my question is, if it's only distorting only when the compression is on, are you perhaps boosting the signal a little with the compressor, therefore overdriving the wah input stage? Maybe you think you're overdriving the amp's input, but it's really the wah. Or the boost from the compressor is compounding with the wah to multiply to a signal that is distorting the amp. Have you tried turning the output down on the compressor? If you like the compressor levels exactly where they are because of how it sounds, then put the wah before it so you don't have to change the compressor settings.
Myself, I always go to the wah first, no matter what the rest of my setup is. I want nothing between the wah and the guitar, just as I don't want compression between me and the preamp either.