If it does, then try to disable the jhb house robots can repair.esp and see if that helps. That is the only mod I can see where it makes a change to the megaton house. If that doesn't work, see if you can remember if any of the weapons in your load order were added to the megaton house and do the same with those.
new load order
Mod load order report
! Warning: current load order template contains 19 duplicate entries
Fallout3.esm
Masterlist Information: $Revision$, $Date$, $LastChangedBy$
Anchorage.esm
ThePitt.esm
BrokenSteel.esm
PointLookout.esm
Zeta.esm (Inactive)
SAS Gear.esp
* This mod does not exist in the current template
MAXdog.esp
* This mod does not exist in the current template
Dogmeat Armor.esp
* This mod does not exist in the current template
HZ_M92SE.esp
10mmReplacer.esp (Inactive)
EssentialFollowers+Caravans.esp
* This mod does not exist in the current template
AK-47_Assault_Rifle.esp
* This mod does not exist in the current template
stat_change_AK-47_Assault_Rifle.esp
* This mod does not exist in the current template
FN_SCAR.esp
* This mod does not exist in the current template
Mini Uzi Suppressed.esp
* This mod does not exist in the current template
KDS M9Beretta With Ironsights.esp
* This mod does not exist in the current template
JHB House Robots Can Repair.esp
* This mod does not exist in the current template
WasteCA.esp
* This mod does not exist in the current template
NightvisionGoggles(Powered).esp
* This mod does not exist in the current template
Urbanized Winter Combat Armor.esp
* This mod does not exist in the current template
Indestructible Weapons and Armor.esp
* This mod does not exist in the current template