The major and minor skills go up, but misc skills don't. It just stays in 0/100. The mods in bold are the ones who change skills. The only 2 that do that (the unarmored one only increases the armor received from unarmored) are wakim's and btb settings.

GameFile0=Aduls_Master_Mod.esm
GameFile1=Bloodmoon.esm
GameFile2=MCA.esm
GameFile3=Morrowind Patch v1.6.5-BETA.esm
GameFile4=Morrowind.esm
GameFile5=Tribunal.esm
GameFile6=TR_Data.esm
GameFile7=TR_Map1.esm
GameFile8=TR_Map2.esm
GameFile9=adamantiumarmor.esp
GameFile10=Adj_Magicka Regen (0.50%).esp
GameFile11=Aduls_Arsenal.esp
GameFile12=AK_PCClothier_Balmora.esp
GameFile13=Always +5 Modifier.ESP
GameFile14=Antares' Big Mod 5.3.esp
GameFile15=AragonMonk-v10.esp -> increases armor gotten from unarmored
GameFile16=B79_RacersRoost_v1.1.esp
GameFile17=BalmoraStockExchange_0925.esp
GameFile18=bcsounds.esp
GameFile19=Bloated Caves.esp
GameFile20=BTB - Alchemy.esp
GameFile21=BTB - Character.esp
GameFile22=BTB - Equipment.esp
GameFile23=BTB - Settings.esp
GameFile24=BTB - Spells.esp
GameFile25=CalderaFightClub.esp
GameFile26=Complete Morrowind - Tribunal & Bloodmoon.esp
GameFile27=Complete Morrowind TB & BM - Replacer.esp
GameFile28=CS Studios Petshop.esp
GameFile29=Dread.esp
GameFile30=EBQ_Artifact.esp
GameFile31=entertainers.esp
GameFile32=Graphic Herbalism.esp
GameFile33=Illuminated Order v1.0 - Bloodmoon Compatibility Extras.esp
GameFile34=Illuminated Order v1.0.esp
GameFile35=Improved Gold Weight.esp
GameFile36=INDYBANK.ESP
GameFile37=LeFemmArmor.esp
GameFile38=master_index.esp
GameFile39=MCA - Guards Patch.ESP
GameFile40=MCA - TR Addon.ESP
GameFile41=MWE_Base.esp
GameFile42=MWE_Writing.esp
GameFile43=NOM 2.13.esp
GameFile44=Piratelords Trade Enhancements.esp
GameFile45=Realistic Weather v2.0.esp
GameFile46=Siege at Firemoth.esp
GameFile47=Skooma Anonymous.esp
GameFile48=SQD_Vile_VampHider.esp
GameFile49=Sris_Alchemy_BM.esp
GameFile50=Suran_Underworld_2.5.esp
GameFile51=TravelingMerchants-1.2_BETA.esp
GameFile52=Vampire Alchemist.esp
GameFile53=Vampire Realism II - BM Add-On.esp
GameFile54=Vampire Realism II - TB Add-On.esp
GameFile55=Vampire Realism II.esp
GameFile56=Vvardenfell Druglord.esp
GameFile57=Wakim's Game Improvements with No-glo v9.esp
GameFile58=Wayfarer's Rest v1.21.esp
GameFile59=Westly's Master Headpack X.esp
GameFile60=ZAS1.esp

Yes, it's BTB settings. There is an Alternate Settings esp in the extras folder that goes back to the vanilla method.

You should not use Wakim's and BTB's together.
BTB's somewhat replaces Wakim's.

Of course BTB settings plugin halt misc skills progression, so you should make it load before that mod of yours about unarmored.

Edit: Ninja'ed