Please follow the steps below
Im going to have you try to get it into bootloader mode manually
1) Unplug your MF3D
2) While holding the four corners of the arcade button grid, connect your Midi Fighter 3D to a USB port, do not use a USB hub.
3) If it works you should see a the right bank button pulse slowly
Remember this can be a little tricky so try again if it doesn't work first time.
4) Download the attached file, should be called MF3D_3D_RESCUE.zip, unzip the file, it will give you a *.Hex, Don't open it, you'll do that in step 7.
5) Run the utility.
6) Click Tools>Midi Fighter>Load Customer Firmware>For a 3D
7) Navigate to the file you downloaded in step 1) and click "Open".
8) The utility will now flash your MF3D and it should now correctly connect to the utility