Ship "landed" in 84km orbit.. But marked as landed on launchpad and uncontrollable

[4d4Garrison]

So today I launched 2 spacecraft into orbit to begin a manned duna mission. I docked the spacecraft, then timewarped for a while to get duna into the right position for a transfer. After the timewarp I clicked on my spacecraft, but noticed something odd, it was shown above kerbins surface, but with no orbit. I figured it was a visual bug and clicked "Fly". The spacecraft had all its RCS firing and I couldn't do ANYTHING with it other than activate lights, landing gear, and brakes. It shows that it has an orbital speed of 199ms and that it is moving at 0ms over the surface. I tried restarting the game, restarting my computer going to a save when I first docked, nothing worked. I can even recover the vessel if I want to as the game is convinced that it is landed on the pad at 84,000km. I also accidentally destroyed the launch pad but now I cannot repair it because the game says the vessel is landed on it..... Does anyone know how to fix this glitch or should I just re-do my mission?

I am using stock KSP and I am not sure how to get the game file, any help with that would be much appreciated!

Pictures:

Note the RCS firing constantly

Note the orbital speed...

Note that I can recover the vehicle

 

Edited March 15, 2016 by 4d4Garrison

[Captain_Miffles]

I know this question is kinda ancient, But i just had the same problem with a buoyant offshore rig.

I flew it out there with jeb in the cockpit and a very low framerate, got in in place, then took jeb on EVA so i could recover him but leave the rig in place.
The instant i hit "recover" on jeb, my game crashed and i had to reload it.

It didn't seem like anything was wrong at first, i was able to ship a few kerbals out to it and it was fully controllable (though not sure if it was frozen in place because it's so heavy i wouldn't expect anything i did at the time to move it)
I realized there was a problem when i tried to launch a different mission and my game told me the rig was on the launchpad...

I am extremely reluctant to actually recover it because it was a monumental pain in the cheeks to get it out there in the first place.
Currently looking for ways to edit the .craft file to tell the game it's splashed down rather than at the launch pad, but if anyone already has a solution i, and i'm sure OP, would be extremely grateful.

[FleshJeb]

@Captain_Miffles Completely offtopic, but that's a gorgeous rig. Do you happen to have any tighter screenshots that show its layout and construction?