Depends quite a bit on the complexity of your robot (e.g. serial chain manipulator vs wheeled robot) and the physics configuration you are using... but it sounds like you are simply running into the limits of numerical stability of your simulation. Increasing the step size too much will make the simulation unstable.

If it is essential to run your simulation with 5ms steps, then you can try adding damping and friction to each of the joints. This may be enough to eliminate the oscillations. You could also try changing from ODE to DART or Bullet. I've had some success with that improving stability in the past.

But be advised that with such a large step time, the physical realism of your sim is going to be pretty poor. 1ms steps are already on the high end for physical realism with Gazebo's default physics settings.