Johannes, I think I may have found a temporary solution for you.
What seems to be happening is that whichever POD Farm plug-in I use, it is somehow splitting the output into two separate (left + right stereo) channels. Even when the track I'm using is
mono.
To be absolutely sure that the effect I was using was supposed to output in mono (even though I knew it should do), I've opened the identical project up in X2 and yes, the output remains in mono.
The only way I've found to return it to mono in X3 is by changing the Interleave button on the track to mono.