Here is the skinny. You can only have one time code master. That's it, nothing else. In your case, the BRC should be it. It will output MTC, ADAT synce, etc....all at the same time and in unison (meaning that is is relational, meaning that MTC actually uses SMPTE as it's time code and the SMPTE is calculated from the ADAT 48K word clock). ADAT's like to be masters in any sync situation, so be it.
Make sure that the BRC is not in EXT SYNC mode.
You only need to output midi from the BRC to your mide input to the computer. Do not return the midi to the BRC because it is not needed, the BRC is creating the clock for your software to run.
Your software needs to be put into EXTERNAL SYNC mode. I don't know how you do that with what you have, but it should have a way to do this. The MIDI IN port on your soundcard/midi card needs to be configured as a MIDI IN. Many different cards supply ports that you can configure.
You need to make sure that the BRC is outputting MTC on the right MIDI channel. This is easy to set. Go to the MIDI/UTIL button and press it until you get the MIDI Device menu on the LCD then set it for whatever channel you are going to use. Your software needs to be configured to accept this channel as the incoming Time Code it is going to use, meaning it needs to be on the same MIDI channel.
The BRC needs to be set to Generate Sync, which is done with the GEN/SYNC buttom. You need to edit this feature to output MTC. Press the EDIT bottom, then the GEN/SYNC bottom until you get MIDI:, then use the uppercase and lowercase buttons to select MTC then exit.
If your software and hardware on the computer is configured right, your computer will now sync to the ADAT relative to SMPTE. Of course you are probably aware of SMPTE Offset and all that so I won't go into that.
Also, if your software will do what I think is called Dynamic Sequencing (where it starts the song at the point of where the incoming SMPTE time code is) then you can cut down on sync time be engaging the Output Rew/FF under the MIDI/Util button on the BRC.
If you are still having problems, then post again.
Ed