I'm having some of the same problems--while my UI doesn't glitch out, I am getting the "Cannot warp under acceleration" despite having RCS, SAS, and engine off. When this glitch begins, my navball also becomes unresponsive (changing the ship's attitude is not reflected on the ball). When I am able to warp (inconsistently), the ship still moves around as though it wasn't warped (typically warping freezes the ships orientation and position, right?); sometimes I can even still control ship movement under warp. Windows 7x64, i5-4690, 8GB, ATI Radeon 4800, through steam. 1.0.3 and 1.0.4 Happens both on old save files and a brand new sandbox I started just to test this problem.