While you are most likely correct, most if not all of them shouldn't, as far as I can tell, be affecting these scripts, so I'm not sure where to begin my troubleshooting
The mod list I'm using is:
3C-FD Patcher
TSLRCM
Fixed Hologram models and Admiralty Redux
TOR Ports KOTOR Comic Republic Uniforms Admiralty Patch
NIM Fix for the KOTOR Comic Republic Uniforms Admiralty Patch
Party Swap
Handmaiden & Disciple Same Gender Romances
Train the Disciple
Train the Handmaiden
Coruscant Jedi Temple
Coruscant Jedi Temple Compatibility patch
Coruscant Jedi Temple Expansion
Galaxy Map[ Fix Pack
Coruscant Map and Textures
Peragus Galaxy Map Change
Kreia Fall In-Game
HK Droids SWTOR Style
Delayed NarShadaa Main Quest
Extended Enclave (With the appropriate patches for Party Swap and Handmaiden & Disciple Same Gender Romance)
HK Factory Alternate Beginning
TSL Lightsaber Pikes
Effixian's Lore Keeper Robes
Effixian's Prototype Knight & Warrior Breastplates
Effixian's Tropper Armors
Effixian's Mandalorian Disguises
Effixian's Red Electromesh Robes
Exiles Armband Force Leap
Maintenance Officer Realistic Reskin
Side Opening Doors on Malachor
Malak's Armor Reskin
Widescreen UI Fix for GOG
Realistic Nar Shaddaa Skybox Mod (& Loadscreens)
Fixed Mandalorian Banners
Remote Tells Influence
Force Affinity Fix and Overhaul
Visas Marr and Female Exile Romance
Workbench Crystal Attunement
Leilukin's Lonna Vash Mod for TSLRCM
JC's Supermodel Fix for K2
Vanila Sabers Patched
Zeison Sha Armor Male Model Fix
Consistent Bastila Recognition
Bounty Hunter Starport Visa Fix
Mira's Vanilla Escape for TSLRCM
Unofficial TSLRCM Tweak Pack (Components 1, 5, & 6)
Revan's Flowing Robes for TSL
No Force Speed Blur for GOG
Originally I thought that the Lonna Vash mod might be affecting the Korriban cave, but then it also happened with Atris vs the Handmaiden & Atton vs Sion.