I don't know if anyone else has notice the same thing as I did today.
Right from the start in my current game I became aware of this and at first I thought it was either MPP 1.6.6 or Class Abilities 3.1 that was causing this, but after some tests I realized that this could be an engine bug and I haven't seen before.
Active Mods
_002_ Tribunal.esm
_003_ Bloodmoon.esm
_004_ Morrowind Patch v1.6.6_beta.esm
_005_ Book Rotate.esm
_006_ Better Heads.esm
_007_ Better Heads Tribunal addon.esm
_008_ Better Heads Bloodmoon addon.esm
_009_ TR_Data.esm
_010_ TR_Mainland.esm
_011_ Wyrmhaven.esm
_012_ Class Abilities 3.1.esp
_013_ Better Bodies.esp
_014_ 20books.esp
_015_ Secret_Master's_Alchemy_Equipment_v1.0.esp
_016_ Dragonbone_Pauldrons.esp
_017_ Lost pieces of unknown armor - Class 04.esp
_018_ Amulet of Icarian flight.esp
_019_ Clean The Apartment.esp
_020_ Balmora Wall House.ESP
_021_ ChaniBalmoraVendor.esp
_022_ Balmora Lockpick and Probe Merchant.esp
_023_ Balmora Soul Gem Merchant.esp
_024_ Bloodmoon Vendor.esp
_025_ hidaway001.esp
_026_ Ghostgate_Sactuary.esp
_027_ LOCH_Strider_Hovel.esp
_028_ Better Balmora river.esp
_029_ Arthmoors_Merchants.esp
_030_ Ashlander_Transports.esp
_031_ The Sable Dragon 1.7.esp
_032_ telbranoramanor.esp
_033_ ImprovedAdamantiumArmor.esp
_034_ CleanAreaEffectArrows.esp
_035_ CleanBitterCoastSounds.esp
_036_ CleanEntertainers.esp
_037_ CleanHelmOfTohan.esp
_038_ CleanMasterIndex.esp
_039_ Master Index Upgrade.esp
_040_ Adamantium Roundshield.esp
_041_ Better Clothes_v1.1_nac.esp
_042_ BetterClothes_Patch.esp
_043_ More Better Clothes.esp
_044_ More Exquisite Clothes.esp
_045_ vince_robe_drakescale.esp
_046_ vince_robe_haazheel.esp
_047_ Sleepers Robe.esp
_048_ Necklace_Pack.esp
_049_ Unique Jewelry and Accessories.esp
_050_ Book Rotate - Morrowind v1.1.esp
_051_ Book Rotate - Tribunal v5.3.esp
_052_ Book Rotate - Bloodmoon v5.3.esp
_053_ Book Jackets - Morrowind - BookRotate.esp
_054_ Book Jackets - Tribunal - BookRotate.esp
_055_ Book Jackets - Bloodmoon - BookRotate.esp
_056_ TravelingMerchants_v2.2.esp
_057_ Thirsk Expanded.esp
_058_ Westly_Presents_Unique_Winged_Twilights.esp
_059_ Passive Wildlife Vvardenfell.esp
_060_ Westly's Master Headpack X.esp
_061_ Sris_Alchemy_BM.esp
_062_ Sri Alchemy BM List Patch.esp
_063_ Books of Vvardenfell.esp
_064_ BB_Grimoires.esp
_065_ COI.ESP
_066_ Atmospheric Plazas.ESP
_067_ Lakeside House.esp
_068_ Imperial Presence.esp
_069_ Pool of Forgetfulness.ESP
_070_ DM_DB Armor Replacer-ExpDDBA.esp
_071_ Glass Gauntlets 10.esp
_072_ Stalhrim Stuff.esp
_073_ wl_dockclutter.esp
_074_ ASH 2.0.esp
_075_ abotWhereAreAllBirdsGoing.esp
_076_ abotSkarPlatforms.esp
_077_ abotLava&Steam.esp
_078_ abotShrines0GoldFix.esp
_079_ abotThunders&Lightnings.esp
_080_ abotGondoliers.esp
_081_ abotBoatsTR.esp
_082_ abotRiverStridersTR.esp
_083_ abotSiltStridersTR.esp
_084_ abotTRWaterSound.esp
_085_ Shashmanu Camp Expanded.ESP
_086_ Seyda Neen Transport.esp
_087_ Clean Aln'Baldrahn.esp
_088_ The regulars - Sitting NPC's v2.02.esp
_089_ LotsOfRings.esp
_090_ LotsOfRingsPlus.esp
_091_ THTWG - Framerate Version.esp
_092_ TyrMagickaRegen.ESP
_093_ md_magebane_replacer.esp
_094_ UFR_v3dot2.esp
_095_ New Randagulf's Fists.ESP
_096_ New Lord's Mail.ESP
_097_ New Umbra.ESP
_098_ XE Sky Variations.esp
_099_ New Suran.esp
_100_ Redaynia Village.esp
_101_ Village of Mora Uvirith v1.2.esp
_102_ Uvirith's Legacy_3.32.esp
_103_ UL_BookJackets_Add-on.esp
_104_ UL_Chess_Add-on.esp
_105_ UL_3.3_MWSE_Add-on.esp
_106_ UL_MWSE_Companions_v2.esp
_107_ UL_3.3_TR_14.08_Add-on.esp
_108_ Nerevarine Urshilaku Tent.ESP
_109_ Salit Camp_Yakaridan Camp - Fixed Door Marker.esp
_110_ Hlormaren - Fixed Dome building.esp
_111_ Dock Walkway_No Building.esp
_112_ Mashed Lists.esp
This is what I did when I tested this in-game with MPP 1.6.6 and in vanilla.
1. Cast the Summon Ancestral Ghost spell then hit it with a http://www.uesp.net/wiki/Morrowind:Silver_Staff_of_Hunger#Silver_Staff_of_Hunger (Telvanni quest reward in vanilla) - Successful
2. Added a Nordic Broadsword via the console and enchanted it with a soultrap spell on strike
3. Cast the Summon Ancestral Ghost spell then hit it with an enchanted Nordic Broadsword (I name it as Nordic Broadsword of Hunger) - No effect
The result for the third step is this http://www.theassimilationlab.com/forums/gallery/image/6760-morrowind-2015-08-13-212004029/, which makes the starting gear you get in Class Abilities 3.1 basically worthless at least the enchanted *normal* weapon (has a soultrap spell on strike) for the enchanter class is just dead weight.
It seems the game engine handles the soultrap spell differently aside from the other spell effects in-game, if you add the soultrap effect when enchanting a normal weapon and I don't think any mod can cause this.