When duplicating multiple parts in both the SPH and VAB, all parts attached to the one I duplicated are offset in random directions and it really slows down larger builds. Here is a simple plane with no offsetting suffering from the bug. I had all of my mods installed before the bug started, so it doesn't seem like they were the problem, but here they are anyway:
BetterTimeWarpContinued (BetterTimeWarpCont 2.3.13)
ClickThrough Blocker (ClickThroughBlocker 1:0.1.10.17)
Distant Object Enhancement Continued (DistantObject v2.0.3.1)
Distant Object Enhancement Continued default config (DistantObject-default v2.0.3.1)
Docking Cam (DockingCamKURS 1.3.8.2)
Docking Port Alignment Indicator (DockingPortAlignmentIndicator 6.10.0.0)
Easy Vessel Switch (EVS) (EasyVesselSwitch 2.3)
Environmental Visual Enhancements - Stock Planet Config files (EnvironmentalVisualEnhancements-HR 2:EVE-1.2.2-1)
Environmental Visual Enhancements Redux (EnvironmentalVisualEnhancements 3:1.11.6.1)
Kerbal Engineer Redux (KerbalEngineerRedux 1.1.9.0)
Kerbal Joint Reinforcement - Next (KerbalJointReinforcementNext v4.1.15)
KSP Recall (KSP-Recall v0.2.2.1)
ModularFlightIntegrator (ModularFlightIntegrator 1.2.10.0)
Module Manager (ModuleManager 4.2.1)
PlanetShine (PlanetShine 0.2.6.6)
PlanetShine - Default configuration (PlanetShine-Config-Default 0.2.6.6)
scatterer (Scatterer 3:v0.0831)
Scatterer Default Config (Scatterer-config 3:v0.0831)
Scatterer Sunflare (Scatterer-sunflare 3:v0.0831)
Toolbar Controller (ToolbarController 1:0.1.9.6)
TweakScale - Rescale Everything! (TweakScale v2.4.6.8)
VesselMover Continued (VesselMoverContinued v1.12.0)
Waterfall Core (Waterfall 0.8.1)
Zero MiniAVC (ZeroMiniAVC 1:1.1.2.4)