1.3.1 RSS/RO/RP1 Parts appearing offset/applying phantom torque

[IncongruousGoat]

KSP version: 1.3.1 Windows 64bit

Problem: Any spacecraft sent beyond low Earth orbit has certain, seemingly randomly selected, parts offset from where they should be. These parts will often result in phantom torque. The phenomenon gets more severe with both longer flight times and greater distances away from Earth.

Mods installed:

Spoiler

FilterExtensions
Toolbar
Advanced Jet Engines
ATK Propulsion Pack
B9 Procedural Wings
B9 Part Switch
BahaSP
BetterBurnTime
BetterTimeWarp
Bluedog DB
Community Category Kita
Community Resource Pack
Connected Living Space
Contract Configurator
Custom Barn Kit
Deadly Reentry
Distant Object Enhancement
DMagic Orbital Science
DMagic Science Animations
Editor Extensions Redux
Engine Group Controller
Environmental Visual Enhancements
FASA
Ferram Aerospace Research
Firespitter
Hangar Extender Extended
Filter Extensions
Janitor's Closet
Kerbal Alarm Clock
KAS
Kerbal Construction Time
KER
KIS
KJR
Kerbal Renamer
Kopernicus
kOS
KRASH
KSC Switcher
KSP-AVC
KSPWheel
MagiCore
MechJeb 2
Modular Flight Integrator
NavyFish Docking Port Alignment Indicator
Near Future Construction
Near Future Electrical
Near Future Propulstion
Persistent Rotation
PlanetShine
Principia
Procedural Fairings
Procedural Parts
RCS Build Aid
Real Chute
Real Engines Pack
Real Fuels
Real Heat
Realism Overhaul
Real Plume
Real Solar System
RemoteTech
Retractable Lifting Surfaces
RP-0 (1.3.1 dev version)
RSSDateTime
RSSVE
SCANSat
Scatterer
Ship Manifest
SmokeScreen
Solver Engines
Soviet Engines
SSTU
SXT
Taerobee
Test Flight
Texture Replacer Replaced
TAC-LS
Transfer Window Planner
Ven's Stock Revamp
Waypoint Manager
Wild Blue Industries

Replication steps: Launch a probe on any BLEO trajectory (the example one is headed to Venus). From some vessel/location other than the probe, warp forward a few months. Switch back to the probe. Observe parts offset when in normal flight but not during time warp.

Screenshots:

Spoiler

An example interplanetary spacecraft en route to Venus at x1 time:

The same spacecraft, at x5 time warp:

Note the suddenly in-place RCS quads and parabolic antenna, the no longer floating experiments, and the shifted solar panels, among several other differences.

Logs: Log files will be provided if requested. I haven't posted them since this problem isn't a crash.

Edited October 8, 2018 by IncongruousGoat