After finally starting Fallout 3 on PC, (got it with a new computer and Oblivion) I decided to get mods after finishing the MQ. Now all has been good and well until the Scientific Pursuits quest. Dr.Li was not in the Rivet City Science Lab and after following the quest marker, I found her in the Citadel exterior. This didn't happen with vanilla so I fear a mod conflict.

Current Load Order:
Fallout3.esm
Anchorage.esm
ThePitt.esm
BrokenSteel.esm
PointLookout.esm
Zeta.esm
CALIBR.esm
FOOK2 - Main.ESM
FOOK2 - [DIK] DLC Improvement Kit.ESM
Mart's Mutant Mod.esm
EnclaveCommander-OA-Pitt-Steel.esm
CALIBRxMerchant.esp
FOOK2 - Main.esp
FOOK2 - [DIK] DLC Improvement Kit.esp
WeaponModKits.esp
WeaponModKits - FOOK.esp
Mart's Mutant Mod.esp
Mart's Mutant Mod - DLC Anchorage.esp
Mart's Mutant Mod - DLC The Pitt.esp
Mart's Mutant Mod - DLC Broken Steel.esp
Mart's Mutant Mod - DLC Point Lookout.esp
Mart's Mutant Mod - DLC Zeta.esp
Mart's Mutant Mod - Hunting & Looting.esp
Mart's Mutant Mod - Increased Spawns.esp
Mart's Mutant Mod - Natural Selection.esp
Mart's Mutant Mod - Tougher Traders.esp
Mart's Mutant Mod - Zones Respawn.esp
Mart's Mutant Mod - FOOK2.esp
Mart's Mutant Mod - FOOK2 - DIK.esp
xCALIBR.esm
xCALIBR_override.esp
xCALIBRmunitions.esp

EDIT:After reloading old save games, problem seems to occur after the start of "Those!" Upon this, I have decided to start a new game. Just one question, do any of these mods affect the quest and Dr.Li's AI?

You need the http://www.fookunity.com/forum/showthread.php?t=3612. The first plugin will send Dr. Li home and set everything straight. Also, It's evident that you're using FOOK2 v1.1 beta plugins and it's imperative that you remove all of the v1.0 compatibility patches.

I see. Well thank you for your support sir. I have used the hot fixes and everything is fine. Just 1 question. How more unstable will the game get with MMM 1.0 compatibility patches instead having no comp patches active?