Having this same problem and can't find any settings to change (except whether or not it's on toolbar and kerbal alarm clock settings). Productivity is 0, don't have enough parts, but ships still build instantly.
I am running 64-bit KSP. Where should I be looking for logs?
Mods I am using:
[x]Science!11
BetterBurnTime
Chatterer
Click Through Blocker
Community Category Kit
Distant Object Enhancement
Distant Object Enhancement default config
Docking Port Alignment Indicator
Easy Vessel Switch (EVS)
Environmental Visuals Enhancements
Extraplanetary Launchpads
Kerbal Alarm Clock
Kerbal Attachment System
Kerbal Engineer Redux
Kerbal Inventory System
Kerbal Stats
Kethane Mining
Kopernicus Planetary System Modifier
LoadingScreenManager
Mechjeb 2
Modular Flight Integrator
Module Manager
PlanetShine
PlanetShine - Default configuration
RasterPropMonitor
RasterPropMonitor Core
SmokeScreen - Extended FX Plugin
TAC fuel Balancer
Toolbar
Toolbar Controller
Trajectories
Tweak Scale