I am using MMM, and ARSENAL together. MMM adds new super mutants while ARSENAL adds lots of new weapons to these new super mutants. I am running the compatibility patch for the two. For some reason super mutants are now spawning without weapons, and the ones added by MMM are spawning with vanilla fallout names( in MMM they spawn and are called Super mutant infantry, now they are just super mutants). They will occasionally spawn with a weapon from arsenal but will not use it instead switching to their fists

here is my load order

Fallout3.esmAnchorage.esmThePitt.esmBrokenSteel.esmPointLookout.esmZeta.esmUnofficial Fallout 3 Patch.esmCALIBR.esmxCALIBR.esmCRAFT.esmEnclaveCommander-OA-Pitt-Steel.esmMothership Crew.esmLings.esmLingsDLC.esmHairPack.esmSydney Follower.espFO3 Wanderers Edition - Main File.esmMart's Mutant Mod.esmARSENAL MOD.esmARSENAL MOD.espAFS Enclave.esmAFS Brisbane.espCrossModData.esmSharing and Caring Companions.esmSkrees_BF2142.espSCC Bunchapeople.espMorepeople.espEvenMorePeople.espJSSpartans.espCrowdedCities_v2.espRealistic Interior Lighting.espRealistic Interior Lighting - OA.espRealistic Interior Lighting - BS.espCRAFT - Activation Perk.espASU.espeyes_hairpack_en.espProject Beauty.espProject Beauty- Broken Steel.espFO3 Wanderers Edition - Main File.espFO3 Wanderers Edition - DLC Anchorage.espFO3 Wanderers Edition - DLC Broken Steel.espFO3 Wanderers Edition - DLC Point Lookout.espFO3 Wanderers Edition - DLC The Pitt.espFO3 Wanderers Edition - DLC Mothership Zeta.espMart's Mutant Mod.espMart's Mutant Mod - Increased Spawns.espMart's Mutant Mod - Feral Ghoul Rampage.espMart's Mutant Mod - Hunting & Looting.espMart's Mutant Mod - Tougher Traders.espMart's Mutant Mod - Natural Selection.espMart's Mutant Mod - Zones Respawn.espMart's Mutant Mod - DLC Anchorage.espMart's Mutant Mod - DLC The Pitt.espMart's Mutant Mod - DLC Broken Steel.espMart's Mutant Mod - DLC Point Lookout.espMart's Mutant Mod - DLC Zeta.espMart's Mutant Mod - FWE Master Release.espARSENAL MOD+Mart's Mutant Mod.espSCC - Talk to Anyone.espFollowersHire.espdD-Full Screen Blood.espdD-Larger Blood.esp1PipboyPDA.espBlackWolf Backpack.espBlackWolf Backpack - Vendor Script Replenish.espBlackWolf Backpack - Blank's Container Patch.espFieldJackets.espAFS Marines.espImmersiveHealth.espZombie Apocalypse.espZombie Apocalypse - Point Lookout.espFO3 Wanderers Edition - Project Beauty.espUnofficial Fallout 3 Patch - Operation Anchorage.espUnofficial Fallout 3 Patch - The Pitt.espUnofficial Fallout 3 Patch - Broken Steel.espUnofficial Fallout 3 Patch - Point Lookout.espUnofficial Fallout 3 Patch - Mothership Zeta.espFO3 Wanderers Edition - UFP Support.espWasteLand HOuse.espARSENAL MOD_i want buy these weapons.espV.A.T.S. Depth of Field v1.0.esp=Medium=MotionBlur1.1.esp=Medium+Close=DOF1.1.espStealth Kills Enabled.espStealth Kills Enabled - Pitt Compatibility.espS.T.A.L.K.E.R. MOD.espGreenWorld.espKelseyCompanion.espDarNifiedUIF3.espSydney Follower - Load Order Fix.espJHBSydneyUpdate.espodstarmor.espODSTcrate.espUPP - Pack 1.espUPP - Beverage Perks.espUPP  - Quest Perks.espUPP - Experience Perks.espUPP - Pack 2.espArmyOfTwo.espCoD_MW2.espRealistic Death Physics.espLOWER-real-thirdpersonview.espairshipfixed.espJackoMilitaryEquipment1.espMart's Mutant Mod - Project Beauty + FWE.espProject Beauty- Point Lookout.espPlerrME2Armour.espreilly_RangerReplacement.espCoD_ArmorReplacement.espPAL - MERGED.espPersonalVertibird.espTotal active plugins: 112Total plugins: 175

i suspect its some kind of leveled list conflict, but im not sure. Any help is very much appreciated

Actually the new super mutant classes are from FWE (SM Infantry, heavy gunner, etc).
The issue is that your load order is in complete dissarray and you have a ton of mods that are overwriting the settings from FWE and MMM.

check the http://sites.google.com/site/fo3wanderersedition/faq, it has a load order template of how exactly you need to load mods.

The issue you have with the super mutant weapons is because you are missing a merged patch(which is a necessity when running this amount of mods). Please also refer to the FWE FAQ how to create a merged patch.

weird, because i have never noticed this problem before, it just started today, and i have not made any recent changes to my load order

i have changed my load order somewhat following the template. is this a better load order?

Fallout3.esmAnchorage.esmThePitt.esmBrokenSteel.esmPointLookout.esmZeta.esmUnofficial Fallout 3 Patch.esmCRAFT.esmCALIBR.esmxCALIBR.esmLings.esmLingsDLC.esmHairPack.esmARSENAL MOD.esmARSENAL MOD.espSkrees_BF2142.espJSSpartans.espCrowdedCities_v2.espAnimy_prostitution.esmMothership Crew.esmFO3 Wanderers Edition - Main File.esmMart's Mutant Mod.esmEnclaveCommander-OA-Pitt-Steel.esmSydney Follower.espAFS Enclave.esmAFS Brisbane.espCrossModData.esmSharing and Caring Companions.esmSCC Bunchapeople.espMorepeople.espEvenMorePeople.espRealistic Interior Lighting.espRealistic Interior Lighting - OA.espRealistic Interior Lighting - BS.espDarNifiedUIF3.esp1PipboyPDA.espProject Beauty.espProject Beauty- Broken Steel.espProject Beauty- Point Lookout.espCRAFT - Activation Perk.espASU.espeyes_hairpack_en.espdD-Full Screen Blood.espdD-Larger Blood.espBlackWolf Backpack.espBlackWolf Backpack - Vendor Script Replenish.espBlackWolf Backpack - Blank's Container Patch.espFieldJackets.espImmersiveHealth.espZombie Apocalypse.espZombie Apocalypse - Point Lookout.espWasteLand HOuse.espARSENAL MOD_i want buy these weapons.espStealth Kills Enabled.espStealth Kills Enabled - Pitt Compatibility.espS.T.A.L.K.E.R. MOD.espGreenWorld.espodstarmor.espODSTcrate.espUPP - Pack 1.espUPP - Beverage Perks.espUPP  - Quest Perks.espUPP - Experience Perks.espUPP - Pack 2.espArmyOfTwo.espCoD_MW2.espRealistic Death Physics.espLOWER-real-thirdpersonview.espairshipfixed.espJackoMilitaryEquipment1.espPlerrME2Armour.espreilly_RangerReplacement.espCoD_ArmorReplacement.espPAL - MERGED.espPersonalVertibird.espFO3 Wanderers Edition - Main File.espFO3 Wanderers Edition - DLC Anchorage.espFO3 Wanderers Edition - DLC Broken Steel.espFO3 Wanderers Edition - DLC Point Lookout.espFO3 Wanderers Edition - DLC The Pitt.espFO3 Wanderers Edition - DLC Mothership Zeta.espMart's Mutant Mod.espMart's Mutant Mod - Increased Spawns.espMart's Mutant Mod - Feral Ghoul Rampage.espMart's Mutant Mod - Hunting & Looting.espMart's Mutant Mod - Tougher Traders.espMart's Mutant Mod - Natural Selection.espMart's Mutant Mod - Zones Respawn.espMart's Mutant Mod - DLC Anchorage.espMart's Mutant Mod - DLC The Pitt.espMart's Mutant Mod - DLC Broken Steel.espMart's Mutant Mod - DLC Point Lookout.espMart's Mutant Mod - DLC Zeta.espMart's Mutant Mod - FWE Master Release.espUnofficial Fallout 3 Patch - Operation Anchorage.espUnofficial Fallout 3 Patch - The Pitt.espUnofficial Fallout 3 Patch - Broken Steel.espUnofficial Fallout 3 Patch - Point Lookout.espUnofficial Fallout 3 Patch - Mothership Zeta.espSCC - Talk to Anyone.espFollowersHire.espAFS Marines.espFO3 Wanderers Edition - Project Beauty.espFO3 Wanderers Edition - UFP Support.espV.A.T.S. Depth of Field v1.0.esp=Medium=MotionBlur1.1.esp=Medium+Close=DOF1.1.espKelseyCompanion.espSydney Follower - Load Order Fix.espJHBSydneyUpdate.espARSENAL MOD+Mart's Mutant Mod.espMart's Mutant Mod - Project Beauty + FWE.espTotal active plugins: 112Total plugins: 175

Better, but the Unofficial Fallout patches are in the wrong place. They belong to the very top of the load order or else they will overwrite the changes of many mods you have loaded.
And like I said you need a merged patch, it's mandatory.

I'm no Mod expert, but from what I understand all ESM files come before any ESP files. I see several ESPs sprinkled among the ESMs. Someone more experienced want to take a crack at this?

they have been set to act as master files using fo3edit.

the merged patch doesnt say finished, it seems to stop at the last mod in my load order, is it meant to do that?

Yes. If it doesn't give an error, it's finished.

after it stopped, did you right click the panel on the left that shows all the mods and select the create merged patch option?
after you create the merged patch and try to close out of FO3 edit you will be asked to name your patch. If you dont get asked to name your patch, then you never created one, you just let FO3 edit "read" all your mods and closed out of it.

now they are actually using the weapons they should. Thank you everyone for the help