I have the same problem. Anyone know if a midi solution thru box fix the amp channel latency?  
M13 to thru box to control switcher. 
  
My setup(4 cable method): 
Line 6 m13  
Mesa boogie dual rectifier  
Voodoo lab control switcher  
 Sennheiser hd400 hum eliminator (send)  
  
Cheers