Alrighty, so here's my mod list currently.
KSP: 1.2 (Win64) - Unity: 5.4.0p4 - OS: Windows 10 (10.0.0) 64bit USI Tools - 0.8.2
Chatterer - 0.9.91.1586
Community Category Kit - 0.1.1
Community Resource Pack - 0.6.1
DistantObjectEnhancement - 1.8
DMagic Orbital Science - 1.3.0.3
DockingCam (KURS) - 1.2.0.2
EditorExtensionsRedux - 3.3.3
Extraplanetary Launchpads - 5.5
Firespitter - 7.4.1
Interstellar Fuel Switch - 2.2.4
RasterPropMonitor - 0.28
Kerbal Attachment System - 0.6
Kerbin Environmental Institute - 1.2
Kerbal Engineer Redux - 1.1.2
HyperEdit - 1.5.3
Kerbal Inventory System - 1.3
KSP-AVC Plugin - 1.1.6.2
KWRocketryRedux - 3.0.20
XT Landertron - 0.15
Final Frontier - 1.2.3.2675
OPT Spaceplane Parts - 1.8.6
Kerbal Planetary Base Systems - 1.1.5
PlanetShine - 0.2.5.2 RCS Build Aid - 0.9
SCANsat - 1.1.6.9
SpaceY Expanded - 1.3
SpaceY Lifters - 1.14
Surface Mounted Stock-Alike Lights for Self-Illumination - 1.3
Kerbal Alarm Clock - 3.8 USI Core - 0.3.2
Karbonite - 0.8.1
Karbonite Plus - 0.7.1
Karibou - 0.3.1
Konstruction - 0.1.5 USI-LS - 0.5.3
Malemute Rover - 0.2
UKS - 0.50 USI Survivability Pack - 0.6
Universal Storage - 1.2.0.1
EVAParachutesAndEjectionSeats - 0.1.6
Water Sounds - 2.2
[x] Science! - 5.1
Still getting the dreaded flicker. I believe the flicker of the contracts, engineering and toolbar menu is restricted to career mode, but a reliable way to reproduce, or at least I've found, is install a few mods which add to the toolbar in editor (Editor extensions, hyperedit, RCS Aid, USI life support). From there, boot up a fresh career mode, and unlock a few research nodes, then upgrade Mission Control to level 2 and get as many contracts as possible. Then cause the flicker bug in VAB/SPH and it *should* recreate the toolbar, contracts and engineering. If it doesn't then let me know and I'll see what else I did. I've tried this on two different career saves and it affected it both times. Through a brief amount of testing I do not believe it can be caused in sandbox mode.
Any problems recreating let me know and I'll help out as best I can. Cheers again, Aus