With the "Additional Shadow Thieves Content" portion of the mod installed:
After siding with Bodhi in Chapter 3, when I go near the Shadow Thief Headquarters (before seizing the Shadow Thief Shipment), the door guard gives his little "ye've made a mistake..." speech and then an invincible, invisible Arkanis Gath shows up and kills the PC (slowly).
So I reloaded and I thought I'd avoid the HQ until I killed Arkanis at the dockside. I take the long way through the Docks and vulnerable Arkanis shows up and I kill him. Later, when I'm on Bodhi's second quest, I go to the HQ, the guard makes his ironically prophetic speech again, and this time an invulnerable, invisible assassin with a short sword of instant-pc-death shows up and kills the PC (quickly). I can never read his name because I die too fast--but his sword sure is shiny.
Anyway, after uninstalling the Shadow Thieves part of the mod, I reloaded my game and the assassin didn't show. I figured that everyone who installed the mod would side with the Shadow Thieves in Chapter 3 so that they could exercise the option of betraying them to Brega in Chapter 6, so it wouldn't get noticed too quickly.
Despite this little mishap, I love this mod. Keep up the good work!