Put the JM4 in the FX Loop for the amp and eventually got it to work.
I have always had the problem, or maybe a design thing, that in order to get the JM4 to record my guitar I have had to turn the backing tracks down to 3% (its lowest setting) and the guitar to 100%. otherwise the backing track completely swamps the guitar.
I have had to do this again in order to get it to work, but at least I have the option of backing tracks.