Yesterday I decided to play around with planes again. I had only researched Aviation so all my planes were pretty basic. Also since I returned to the game the whole aviation part progression on the tech tree got changed so all my old planes were unusable. I only built one since the update. I remember struggling to build even the basic plane due to lack of the radial air intake and those small MK0 engines since I never built planes like that before.
So yesterday I open SPH and notice there's a bigger jet engine in my part list (J-33 Basic Jet Engine - the one that was there before 1.0.5). Did I completely miss it before ? I must have. I spent so much time trying to make those small 'Juno' engines work and this was here all along ?? So I put it on my plane - flew around a bit and decided to research Aerodynamics tomorrow since I basically didn't have any crucial things I needed to unlock right now.
Today I researched Aerodynamics and decided to fly around in my improved plane a bit to really test out how this 'new old engine' works on it. It was a little too strong but I broke Mach 1 for the first time :) I landed and suddenly noticed that my cockpit is now the OLD model ! I didn't even notice before ! I went back to the hangar and on the part list I see the new cockpit. I can put it on the plane (even NEXT to the old one) but when I launch it always switches to the old one.
I went through all the parts lists and noticed:
- The small landing gear has the old model on the parts list - new model on the plane.
- I'm missing the new J-33 turbofan engine - instead I have the old J-33 Basic Jet Engine. It was there before I researched Aerodynamics and I could use it side-by-side with the new J-20 Juno engines.
- When I put the new MK1 cockpit on the plane, do something else, and then pres Ctrl + Z it wlll instantly switch to the old model.
- Whenever I launch a plane it will switch all Mk1 cockpits to old models. Doesn't matter if the plane design is old or new.
- In my R&D under 'Aviation' there's like 50 Mk1 cockpits listed (alternating between old and new) and under Aerodynamics there's multiple Engine Nascelle's and J-33 Engines (both old models) but not as many as the cockpits.

I tried reloading earlier quicksave. I redownloaded and reinstalled the game (through Galaxy). Nothing helps.
Any help appreciated.

Thats because you did not remove all the runtime data.

remove the game from the system or any local directory,
remove ksp runtime/application data in your home directory (for Linux, its ~/.config/unity3d/),
reinstall,
start a new game - no old saves,
if you use any mods - make sure they are:
a) compatible
b) you use module manager
c) there is only ONE copy of module manager dll, and its inside root of Gamedata - and nowhere else)

I managed to fix it by choosing 'Also remove save games and any game data' while uninstalling through Galaxy (ofc I backed up my savegames first). Looks fine for now at least.
Looks like Galaxy has trouble updating/verifying KSP which is really annoying.

Yeah, thats exactly what runtime/application data stands for.

KSP is technically a scenario, that is run (played) by a game engine (unity3d).
From 1.05 to 1.1, the engine player was updated from v4 to v5.

So, you were running v5 using configs from v4, which leads to all kinds of weirdness. Most annoying being physics going crazy.

Just for the lulz, I find that how you and that guy on the linked video called the thread/video, is confusingly awesome ^)

Wait, will this fix the landing gear on planes going haywire while standing on the runway ? Or struts and rover wheels exploding when touched by a kerbal ?

Don't confuse different things. Run completely new game on old configuration - and stuff will explode instanding, the physics in unity5 ( ksp 1.1.x) is completely different - and much more efficient in CPU overhead. If you do this, this is not KSP fault.

Landing gear, is KSP issue - but more like Unity5 issue. Because physics change, landing gear now behaves differently (actively) when landing. Use this mod and read the reason of the issue here.
Some easily worked around the landing gear problems by just following this guide. At the core of the problem, if the gear is overloaded, it collides into the fuselage with resulting physics force going haywire. And this happens if the weight of the plane is too much for the gear or the landing VERTICAL speed is too much.

Anyways, I would also get this to fix the left issues.