I am on a fresh install of windows, and a fresh download of the game (from the main game thread) and your mod (from your OP). My persistent file (and only the persistent file) was downloaded from this post
https://f95zone.to/threads/being-a-dik-v0-9-1-dr-pinkcake.25332/post-5618683
Taking your advice into account, I nuked my save game folder from both the game directory and the C:\Users\****\AppData\Roaming\RenPy directory. (Since my persistent file... and unfortunately those saves... were the only thing that could be considered dirty with my current setup).
I then proceeded to do a clean speed run to the Troy fight using the same choices I used before.
I didn't initially experience the issue I described, however was finally able to reproduce it after save scrumming a few times.
Lets just say its an extreme edge case that few will ever probably experience.
Basically, I have "Skip Unseen Text" enabled under dialogue in the options menu. Hitting "ctrl" and clicking quickly anywhere in the scene at just the right time during the fight seems to be what is trigging the issue I'm experiencing.
My clean save directory is attached if you want to take a look, but really the issue seems to be solved by slowing my ass down at those scenes.