This problem came about a week ago and I've managed to deal with it up until the gun totally disappeared. First it was transparent but only when I didn't aim down the sights then it turned invisible but only in First Person. Like I said I managed to deal with this but now its completely messed up. Heres my Load Order:

Fallout3.esm
Anchorage.esm
ThePitt.esm
BrokenSteel.esm
PointLookout.esm
Zeta.esm
CALIBR.esm
StreetLights.esm
EVE.esm
DCInteriors_ComboEdition.esm
FCOMaster.esm
CALIBRxMerchant.esp
FOOK2 - Main.esp
FOOK2 - [DIK] DLC Improvement Kit.esp
Aliens Pulse Rifle.esp
FineLeatherCoat.esp
GasMask.esp
BeardsofFallout.esp
SkullMask.esp
gasmaskhelmet.esp
URWLENB-002-Interiors.esp
R.A.C.E. Station.esp
BetterGamePerformance.esp
BlackWolf Backpack.esp
BlackWolf Backpack - Vendor Script Replenish.esp
BlackWolf Backpack - Blank's Container Patch.esp
Wasteland Soldier Armor.esp
Wills Power Armor.esp
Enhanced Shaders.esp
majormodder's Junk Food to Barbeque Crisps.esp
Fellout-Full.esp
Fellout-Zeta.esp
Fellout-PointLookout.esp
Fellout-pipboylight.esp
Fellout-BrokenSteel.esp
Fellout-Anchorage.esp
DYNAVISION - Dynamic Lens Effect.esp
F3ProjectRealityMkI.esp
dD - Enhanced Blood Main.esp
PureWater-VeryClearNoRad-.esp
PureWater-VeryCleanLittleRad-.esp
PureWater-NoRad-.esp
PureWater-LittleRad-.esp
CrowdedCities_v2_lessNPCs.esp
CrowdedCities_v2.esp
RubblePilesFix.esp
colossus T51c.esp
GNR Enhanced.esp
101CombatArmor.esp
Ranger of the Wastes =D.esp

Total active plugins: 50
Total plugins: 66

I can already see some problems with it and i'll update it as soon as I can.

For starters, what mod manager do you use? I do not see a merged patch. Also, there looks like a few redundant esp's installed.

Raed