While I believe the Axe is a great piece of work, I don't believe it's designed to work well in a 4CM mode. I did some extensive testing last night using my JVM410 and it didn't get anywhere close to something that sounded decent unless I used low gain stomp boxes prior to input to the JVM.
There is absolutely nothing about the axe that inhibits it from being used in the 4cm. If you are getting colored sounds (with shunts or effects bypassed) from the axe fx you simply do not have it set up correctly. Are you using global eq? Are you using front input?
Sorry, it is not my intention to sound harsh but the axe is virtually transparent, gain levels are abundantly manipulated and the unit is excedingly quiet. The effects are state of the art.
There are numerous people using the axe in a 4cm and some of them make there living playing the guitar - some are among the best in the field.
http://www.petrucciforum.com/forums/showthread.php?t=68428
Why are others successfully using the axe fx in the 4cm?
It must certainly be capable, possibly even state of the art, when such players as JP choose it for thier gear, right?