Thanks for the input joshuabri. I figured out what my problem was: Bitdefender was preventing tsMuxeR from modifying the mkv, but wasn’t telling me about it.
I now have BDMV and Certificate folders, but ImgBurn is warning me that there isn’t enough room on a BD25 (it’s about 800MB over for Ep1). I’m going to attempt an overburn and hope for the best.