Damn! It's a stupid bug. I think it happens only when there are several subtitle streams to decode and the option to mux the 2D files is ticked in tab 2. Anyway, I have fixed the bug. Or at least I think so. I haven't enough time to test it. Please do it.
Thanks for the bug report!
Code:
# v0.53 (October 23, 2014)
# - Last minute bug fix: Problem when adding the 2D subtitle streams to the _MUX_*D_OPTIONS.txt files
Download:
BD3D2MK3D.7z