We can check your project if you provide us with your VST Transit username (not your mySteinberg username) and the name of the project. We don‘t acess any of your media, just check the data logic. You can send a PM if you prefer so.
I would suggest to go step by step, try MIDI only first, then audio at 48k to see if there is a difference. From your description, it is hard to tell what your actual problems are. Also make sure all tracks that should be transmitted are checked in the transfer list.