Actually, 3 SH3 ShipWake controllers come with stock UBM (on the german torps)...
[edit] But regarding the problem, I doubt it is related to JSGME in this case. It can't be responsible for a sudden change in how the torpedo wake looks. Something went fubar along the line of what you were doing. As suggested, track back your changes, and/or replace the wake controller of the problematic torp with one of another torpedo that works.