At first, I thought this would be a problem relating to BTB Settings or GCD, the two mods I know have a big impact on skill progression. So I decided to do a bit of experimenting with them. To my dismay, I found that using the Alternative BTB Settings mod only made the situation worse. Using BTB Settings (The original one) without GCD did not fix it, nor did using GCD without BTB Settings improve things. And as you might guess, removing both mods did not work.
I don't really know where to go from here, since I don't know what other mod could have such a big impact on skill progression other than those two. If anyone could provide a bit of advice. As you can tell, playing a game where misc skills raise almost instantly is a bit of a hassle, and I really want to nip this in the bud before starting a new character.
Here is a mod list:
Spoiler
Masters for test0000.ess:
001 Morrowind.esm
002 Tribunal.esm
003 Bloodmoon.esm
004 Bloodmoon Landscape Overhaul 1.0.esm
005 Morrowind Patch v1.6.5-BETA.esm
006 abotWaterLife.esm
007 Better Heads.esm
008 Better Heads Tribunal addon.esm
009 Better Heads Bloodmoon addon.esm
010 GDR_MasterFile.esm
011 Texture Fix 1.8.esm
012 MW_Children_1_0.esm
013 MCA.esm
014 WeatheredSigns.esp
015 Lgnpc_SN.esp (Version 0.31)
016 Moreclasses_0605.esp
017 LeFemmArmor.esp
018 LGNPC_NoLore_v0_83.esp (Version 0.83)
019 Atmospheric Sound Effects (BMS Edit).esp
020 Atmospheric Sound Effects - TB (BMS Edit).esp
021 Atmospheric Sound Effects - BM (BMS Edit).esp
022 VGreetings-Hit.esp
023 VGreetings-Thief.esp
024 AV_female_armor.esp
025 AV_fem_armor_Trib.esp
026 VGreetings-Flee.esp
027 VGreetings-Idle.esp
028 VGreetings-Attack.esp
029 VGreetings.esp
030 Disease.esp
031 Less Annoying Guards - Tribunal and Bloodmoon.esp
032 P.R.E. v4.0.esp
033 Better Bodies.esp
034 Nymeria's Monthly Respawn.esp
035 Grave Goods.esp
036 MWE_Combat.esp
037 MWE_Base.esp
038 Windows Glow.esp
039 BetterBooks_AlchFormfix.esp
040 Haunted Tombs v1.06.esp (Version 1.06)
041 Quick Char.esp (Version 1.2)
042 EcoAdjDaedricDrops.esp
043 Healing.esp
044 Pelagiad Fix.esp
045 abotWhereAreAllBirdsGoing.esp
046 IceNioLivRobeReplacerPLUS.esp
047 DB Armor Reducer.esp
048 Mixed Guards 2.esp
049 KS_Julan_Ashlander Companion_1.3.esp (Version 1.3)
050 Less_Generic_Bloodmoon.esp (Version 1.2)
051 LGNPC_GnaarMok_v1_10.esp (Version 1.10)
052 LGNPC_MaarGan_v1_20.esp (Version 1.20)
053 LGNPC_AldVelothi_v1_20.esp (Version 1.20)
054 DN-GDRv1_NOM.esp (Version 1)
055 Westly's Master Headpack X.esp
056 LGNPC_HlaOad_v1_32.esp (Version 1.32)
057 Creatures.esp
058 Go To Jail 3.5 - T B - MCA - NOM.esp
059 Improved Gold Weight.esp
060 LGNPC_Aldruhn_v1_20.esp (Version 1.20)
061 LGNPC_Aldruhn_v1_20_suppl.esp
062 Spect Sorcery pt 1.esp
063 LGNPC_Pelagiad_v1_22.esp (Version 1.22)
064 LGNPC_TelMora_v1_20.esp (Version 1.20)
065 LGNPC_Khuul_v2_10.esp (Version 2.10)
066 Corean_Hair_in_Morrowind.esp
067 LGNPC_VivecFQ_v2_10.esp (Version 2.10)
068 LGNPC_TelUvirith_v1_20.esp (Version 1.20)
069 LGNPC_SecretMasters_v1_30.esp (Version 1.30)
070 LGNPC_IndarysManor_v1_51.esp (Version 1.51)
071 LGNPC_VivecRedoran_v1_50.esp (Version 1.50)
072 Less_Generic_Nerevarine.esp (Version 1.21)
073 LGNPC_PaxRedoran_v1_20.esp (Version 1.20)
074 LGNPC_SoulSicknessPatch_v1_00.esp (Version 1.00)
075 Bloated Caves.esp
076 Graphic Herbalism.esp
077 Graphic Herbalism Extra.esp
078 EcoAdjMerchantSkills (Disposition Edit).esp
079 EcoAdjCrime (Tresspass Edit).esp
080 New Argonian Bodies - Mature.esp
081 New Khajiit Bodies - Mature.esp
082 Less_Generic_Tribunal.esp
083 almalexia armor.esp
084 Windows Glow - Tribunal Eng.esp
085 BTB - Spells.esp
086 BTB - Equipment.esp
087 Better Clothes Complete (BTB Edit).esp
088 The Imperial Legion Badge.esp
089 GCDWhittleUb.esp
090 FemaleEbonyCuirass_TB.ESP
091 FemaleGlassCuirass.ESP
092 FemaleDaedricCuirass.ESP
093 FemaleDragonscaleCuirass.ESP
094 NoM_Creatures Loot PHW.esp
095 FemaleLordsMail_TB.esp
096 MCA - Guards Patch.ESP
097 NoM_CoM Compatibility Patch.esp
098 Water Level Fix - Full.esp
099 NOM 3.0.esp (Version 3.00)
100 Service_Requirements_V1.4.3 (BTB Edit).esp
101 What Thieves Guild.ESP
102 Little Secrets.ESP
103 BB Dark Brotherhood by Westly.esp
104 UniqueFinery_NoRobe.esp
105 LCV Schedule Markers.esp (Version -02)
106 NPC LCV Schedules 03.esp (Version 03-13)
107 NPC LCV Locks.esp
108 Passive_Healthy_Wildlife.esp
109 BTB - Character.esp
110 BTB - Settings (Alternate).esp
111 BTB - Alchemy.esp
112 horationpcenhanced12-bm.esp
113 TLM - Complete.esp
114 WA_SoulGems(!).esp
115 Mashed Lists.esp
001 Morrowind.esm
002 Tribunal.esm
003 Bloodmoon.esm
004 Bloodmoon Landscape Overhaul 1.0.esm
005 Morrowind Patch v1.6.5-BETA.esm
006 abotWaterLife.esm
007 Better Heads.esm
008 Better Heads Tribunal addon.esm
009 Better Heads Bloodmoon addon.esm
010 GDR_MasterFile.esm
011 Texture Fix 1.8.esm
012 MW_Children_1_0.esm
013 MCA.esm
014 WeatheredSigns.esp
015 Lgnpc_SN.esp (Version 0.31)
016 Moreclasses_0605.esp
017 LeFemmArmor.esp
018 LGNPC_NoLore_v0_83.esp (Version 0.83)
019 Atmospheric Sound Effects (BMS Edit).esp
020 Atmospheric Sound Effects - TB (BMS Edit).esp
021 Atmospheric Sound Effects - BM (BMS Edit).esp
022 VGreetings-Hit.esp
023 VGreetings-Thief.esp
024 AV_female_armor.esp
025 AV_fem_armor_Trib.esp
026 VGreetings-Flee.esp
027 VGreetings-Idle.esp
028 VGreetings-Attack.esp
029 VGreetings.esp
030 Disease.esp
031 Less Annoying Guards - Tribunal and Bloodmoon.esp
032 P.R.E. v4.0.esp
033 Better Bodies.esp
034 Nymeria's Monthly Respawn.esp
035 Grave Goods.esp
036 MWE_Combat.esp
037 MWE_Base.esp
038 Windows Glow.esp
039 BetterBooks_AlchFormfix.esp
040 Haunted Tombs v1.06.esp (Version 1.06)
041 Quick Char.esp (Version 1.2)
042 EcoAdjDaedricDrops.esp
043 Healing.esp
044 Pelagiad Fix.esp
045 abotWhereAreAllBirdsGoing.esp
046 IceNioLivRobeReplacerPLUS.esp
047 DB Armor Reducer.esp
048 Mixed Guards 2.esp
049 KS_Julan_Ashlander Companion_1.3.esp (Version 1.3)
050 Less_Generic_Bloodmoon.esp (Version 1.2)
051 LGNPC_GnaarMok_v1_10.esp (Version 1.10)
052 LGNPC_MaarGan_v1_20.esp (Version 1.20)
053 LGNPC_AldVelothi_v1_20.esp (Version 1.20)
054 DN-GDRv1_NOM.esp (Version 1)
055 Westly's Master Headpack X.esp
056 LGNPC_HlaOad_v1_32.esp (Version 1.32)
057 Creatures.esp
058 Go To Jail 3.5 - T B - MCA - NOM.esp
059 Improved Gold Weight.esp
060 LGNPC_Aldruhn_v1_20.esp (Version 1.20)
061 LGNPC_Aldruhn_v1_20_suppl.esp
062 Spect Sorcery pt 1.esp
063 LGNPC_Pelagiad_v1_22.esp (Version 1.22)
064 LGNPC_TelMora_v1_20.esp (Version 1.20)
065 LGNPC_Khuul_v2_10.esp (Version 2.10)
066 Corean_Hair_in_Morrowind.esp
067 LGNPC_VivecFQ_v2_10.esp (Version 2.10)
068 LGNPC_TelUvirith_v1_20.esp (Version 1.20)
069 LGNPC_SecretMasters_v1_30.esp (Version 1.30)
070 LGNPC_IndarysManor_v1_51.esp (Version 1.51)
071 LGNPC_VivecRedoran_v1_50.esp (Version 1.50)
072 Less_Generic_Nerevarine.esp (Version 1.21)
073 LGNPC_PaxRedoran_v1_20.esp (Version 1.20)
074 LGNPC_SoulSicknessPatch_v1_00.esp (Version 1.00)
075 Bloated Caves.esp
076 Graphic Herbalism.esp
077 Graphic Herbalism Extra.esp
078 EcoAdjMerchantSkills (Disposition Edit).esp
079 EcoAdjCrime (Tresspass Edit).esp
080 New Argonian Bodies - Mature.esp
081 New Khajiit Bodies - Mature.esp
082 Less_Generic_Tribunal.esp
083 almalexia armor.esp
084 Windows Glow - Tribunal Eng.esp
085 BTB - Spells.esp
086 BTB - Equipment.esp
087 Better Clothes Complete (BTB Edit).esp
088 The Imperial Legion Badge.esp
089 GCDWhittleUb.esp
090 FemaleEbonyCuirass_TB.ESP
091 FemaleGlassCuirass.ESP
092 FemaleDaedricCuirass.ESP
093 FemaleDragonscaleCuirass.ESP
094 NoM_Creatures Loot PHW.esp
095 FemaleLordsMail_TB.esp
096 MCA - Guards Patch.ESP
097 NoM_CoM Compatibility Patch.esp
098 Water Level Fix - Full.esp
099 NOM 3.0.esp (Version 3.00)
100 Service_Requirements_V1.4.3 (BTB Edit).esp
101 What Thieves Guild.ESP
102 Little Secrets.ESP
103 BB Dark Brotherhood by Westly.esp
104 UniqueFinery_NoRobe.esp
105 LCV Schedule Markers.esp (Version -02)
106 NPC LCV Schedules 03.esp (Version 03-13)
107 NPC LCV Locks.esp
108 Passive_Healthy_Wildlife.esp
109 BTB - Character.esp
110 BTB - Settings (Alternate).esp
111 BTB - Alchemy.esp
112 horationpcenhanced12-bm.esp
113 TLM - Complete.esp
114 WA_SoulGems(!).esp
115 Mashed Lists.esp