User R0j0hound mentioned it could be a bug with the physics joints. He's far more clued up than I am with the technical side of things, so just in case it is a bug, I'm posting it here.
R0j0hounds reply [quote]It looks like it's a bug with joints. I landed on a higher ledge and the orange box just sat above the rocket like you said. The joint offsets aren't the same at different positions.[/quote]
Here's a demo of the CAPX showing what I mean. Move the ship above the block, then thrust up the screen and you'll see the problem.
AMD 645 Athlon X4 Black Edition
Nvidia 560 ti graphics card
Windows 7 64
Google Chrome Version 23.0.1271.40 beta-m (have tried with none beta version too and IE9)
And here's the CAPX so you can have a proper look at what's going one.
EDIT just added system specs and browser info etc.