Wasn't sure where else to report this, but I have the GOG version (most recent patch), and when I cleared the Chapter II Prologue with max points, the game locks up on a black screen instead of showing the intended bonus screen. Seems consistent on my end, I can't tell you much more than that!
A few other people at GOG have also mentioned the error, the ending doesn't seem to matter like I originally thought:
https://www.gog.com/forum/faith_the_unholy_trinity/freezing_on_chapter_2_prologu...