Could it be that it isn't related to any mods? Is this a symptom of savegame corruption?
Spoiler
Active Mod Files:00 Fallout3.esm01 Anchorage.esm02 ThePitt.esm03 BrokenSteel.esm04 PointLookout.esm05 Project Beauty.esm06 Vault 101 Revisited.esm07 CubeExperimental (EN).esm08 RatTrapRemastered.esm09 Mart's Mutant Mod.esm0A Xepha's Dynamic Weather.esm0B EnhancedChildren.esm0C AliciasCuteShop.esm0D Sydney Follower.esm0E Stop Insulting Me Outcasts.esp0F DK_BulletTime.esp [Version 1.0.3]10 Sprint Mod.esp11 GalaxyNewsRadio100[M].esp12 PowerArmorTraining.esp13 The Mantis Imperative - Mantis.esp [Version 1.08]14 RatTraqeyeCandy.esp [Version 1.0]15 RatTrapRadio.esp [Version 1.0]16 RatTrapSound.esp [Version 1.0]17 AQFH.esp [Version 1.05]18 Explosive Entry.esp19 PortableMattress.esp1A UndergroundHideout.esp1B AliciasCuteShopDoorOverride.esp++ TeslaForGirls.esp1C Childhood Beginning.esp [Version 4]1D Mart's Mutant Mod.esp1E Mart's Mutant Mod - DLC Anchorage.esp1F Mart's Mutant Mod - DLC The Pitt.esp20 Mart's Mutant Mod - DLC Broken Steel.esp++ Mart's Mutant Mod - DLC Point Lookout.esp++ Mart's Mutant Mod - Zones Respawn.esp++ Mart's Mutant Mod - Tougher Traders.esp++ Mart's Mutant Mod - Natural Selection.esp++ Mart's Mutant Mod - Master Menu Module.esp21 Mart's Mutant Mod - Project Beauty.esp22 Fellout-Full.esp++ Fellout-BrokenSteel.esp23 Fellout-PointLookout.esp++ Sydney Follower - Load Order Fix.esp24 FelloutNightsRestored.esp25 PowerArmorTraining_Linden.esp26 Cleaning up the trash in Fort Independence.esp27 KarmaThresholdExtreme1010.esp++ Expanded Vendor Inventory.esp++ Ammo Box Respawn.esp++ medkit and toolbox respawn.esp++ My Female Power Armor.esp++ My Female T51b Armor.esp++ My Respawning Nuka Machines.esp++ My Many Containers Respawn.esp++ My Hit Squad Requirement Gimp.esp28 My Increased Weapon Damage.esp29 TheOutcastCollectionAgent.esp** Dr. Li is 37 and Hot.esp++ Defender Morgan is Hot.esp2A Magic Fingers Perk No Karma.esp2B Realistic Sneak Mod.esp** Star Paladin Cross is 37 and Latin.esp** Sydney is Hot.esp2C Bashed Patch, 0.esp
This began happening a little after The Pitt and Operation Anchorage were installed. I noticed it happening each time when playing with The Project enabled. It is now disabled, but that hasn't helped.