I only started having this problem after doing a fresh install of Morrowind to make it stable. Whenever I Exit Morrowind the pop-up of 'Morrowind has stopped working' appears. I tried using compatibility settings and run as admin but it doesn't solve the problem. This is a list of currently active plug-ins and I'm using MGSO v3 patched.
GameFile0=Bloodmoon.esm
GameFile1=Morrowind Patch v1.6.6_beta.esm
GameFile2=Morrowind.esm
GameFile3=Poorly Placed Object Fix 1.2.esm
GameFile4=TR_Data.esm
GameFile5=TR_Mainland.esm
GameFile6=Texture Fix - Bloodmoon 1.1.esm
GameFile7=Texture Fix 2.0.esm
GameFile8=Tribunal.esm
GameFile9=AtmosphericSoundEffects-3.0-Tribunal.esp
GameFile10=Barabus' fireplaces 2.esp
GameFile11=Better Bodies.esp
GameFile12=Better Clothes_v1.1.esp
GameFile13=Better Skulls.ESP
GameFile14=Better Weapons and Armors.esp
GameFile15=BetterClothesForTB.esp
GameFile16=Better_Sounds.esp
GameFile17=Bloated Caves.esp
GameFile18=Book Jackets - Bloodmoon.esp
GameFile19=Book Jackets - Morrowind.esp
GameFile20=Book Jackets - Tribunal.esp
GameFile21=Clean Combat Angle Adjustment.esp
GameFile22=Clean MCFC_1.0.esp
GameFile23=ExcellentMagicSounds.esp
GameFile24=Female Armor - Complete.esp
GameFile25=Golden Gold.esp
GameFile26=Graphic Herbalism.esp
GameFile27=JEB_muffin_fix.esp
GameFile28=KS_Julan_Ashlander Companion_2.0.esp
GameFile29=Key Replacer Trib & BM.esp
GameFile30=LeftGloves_Addon_v2.esp
GameFile31=LevelersBroomCloset.ESP
GameFile32=MA_snowprincetomb_v3.esp
GameFile33=MW Containers Animated.esp
GameFile34=Merged_Objects.esp
GameFile35=More Better Clothes.ESP
GameFile36=Morrowind Code Patch Showcase.esp
GameFile37=Neo's Unique Creatures.esp
GameFile38=New Bodies - Clean.esp
GameFile39=New Voices.esp
GameFile40=NewBlood_MwTbBm1.1.esp
GameFile41=OTR_Coast_Variety.esp
GameFile42=PSsorticon.esp
GameFile43=Particle Arrow Replacer.esp
GameFile44=Psy_UniqueDremora_T.esp
GameFile45=Psy_VGR_Armour.esp
GameFile46=STA_guides_replacer.esp
GameFile47=Shieldfx.esp
GameFile48=SirLuthor-Tools.esp
GameFile49=Sleepers, Awake!.esp
GameFile50=SneakingRealism_En_v3.esp
GameFile51=Statue Replacer - Normal.esp
GameFile52=UF_HortRobeF001.esp
GameFile53=Unique Banners and Signs.esp
GameFile54=Unique Jewelry and Accessories.esp
GameFile55=UniqueFinery.esp
GameFile56=Vampire_Embrace.esp
GameFile57=WA_Signy_Signposts(!).ESP
GameFile58=Windows Glow - Bloodmoon Eng.esp
GameFile59=Windows Glow - Raven Rock Eng.esp
GameFile60=Windows Glow - Tribunal Eng.esp
GameFile61=Windows Glow.esp
GameFile62=abotWindowsGlow.esp
GameFile63=almalexia armor.esp
GameFile64=bones.esp
GameFile65=correctUV Ore Replacer 1.0.esp
GameFile66=guarskin_drum_replacer.esp
GameFile67=imperial chain fix.esp