I've been chasing my tail on this for a few weeks so its time to bring in outside help. I'm running my FM3 in 4CM into a 5150III 50w head. When I run a preset that bypasses the amps head in favor of a amp model as the pre-amp I get this noticeable mid hump, almost cocked wah. I'm running the amp model with power amp turned off and no cab block. Any ideas where else I can check for what might be causing this?
I would first save the amp block to your block library.
Next, build a preset with just an input block, the amp block (select the one you just saved to the block library), and an output block (output 2 with the FM3 so you can use its 1/4" jack). Run output 2 directly to the loop return on your amp.
This condenses it right down to the bare bones, so you can see where you stand with nothing else in the chain.
Does it still have that mid hump? If so, first check to see that the "fat" parameter is not selected (I believe it's in the preamp menu). That parameter will definitely cause a midrange bump.
If it is off, try turning down the midrange knob on the top (authentic) menu.
If that doesn't help, move to the output EQ menu (still in the amp block) and start cutting the midrange there. Start with one slider (around 600Hz or so), and drop it about 6dB or so. If it isn't the frequency that's annoying you, return that slider to zero and move up to the next one. Repeat this until you find the offending frequency, then cut it to taste.
Resave that amp block to the library, then go back to your original preset and replace the original amp block with the one that you just tweaked.