Orbiter uses numerical integration methods for propagating spacecraft states from one simulation frame to the next. The accuracy of this method depends on the simulation time interval between frames. While Orbiter's numerical implementation is quite sophisticated (including high-order Runge-Kutta and symplectic integrators, and subsampling of time steps), it may still lead to problems when extreme time accelerations are used during high-acceleration phases of a spacecraft (e.g. in low orbit).
It is generally a good idea to avoid high time accelerations when in low orbit, and in particular during powered flight. Orbiter also provides an "orbit stabilisation" mechanism that disables the numerical state integration in critical phases. Orbit stabilisation can be configured in the "Extra" tab of the Orbiter Launchpad.