i had a similar issue.
I use MFD extractor to get all the bit to fill helios, but i had to tell BMS to extract at least thing from the main software.
I had it render at 10x10 so it was really small.
This forced windowed mode and got rid of the black screen, but i managed to trick BMS in conjunction with SOFTTH.net to get rid of the top border so it appears fullscreen.