Just thought that I'd offer a bit of insight on this topic. I am a Power Engineer, not an EC, but this is my area of specialisation.
The VFD is likly not doing anything to cause the conduit heating (unless it is malfunctioning). The two conduits are carying the same net current:
Left Conduit:
125<120 A + 125<-120 A = 125<180 A
Right Condit:
125<0 A
If you were to total the two current you would get 0, this is why we combine all 3 phases (and neutral if aplicable) in the same conduit.
The metalic conduit is acting as a curent transformer, the net current in the conductors is inducing a current in hte conduit and because there is a second ground path (the EGC) this current can flow and heats the conduit by P=I^2R.
As you all know the correct way to do this is to split the conductors into two ABC groups. I hope some one will be fixing this.
The only reasons that I can come up with for one being hotter is either a bad bond an one end of the cold counduit or the EGC is carying current.
