I think the mods folder was added during this update, as such the TFMM does not install mods correctly unless there is a new version out after the dlc was released. At least thats what i think.
I got some info and got it working. Go to Train-fever.net and download my NSB Stadler Flirt v1.6.1. It’s working with the new version of the game. You’ll see how it’s done there.