Anim8or, and other programs, have certain rules regarding rotation. Sometimes you need to put some interim steps between your 90-degree way points, because from a strictly mathematical point of view, it may calculate that there's a quicker way to get from point X to point Y, which involves rotating about another axis. So, sometimes you need to force the key frames to go the way you want.
Another phenomena is gimbal lock, and it's the bane of not only modelers, but any mechanism where the axes of a multi-axis system can line up with another axis. It has to do with how you reference an object's local axes with those of the outside (or world) environment.
From a static, local point of view, the X-, Y-, and Z- axes are always orthogonal (separated by 90 degrees) to each other. If you rotate an object along its X-axis only, once it rotates 90 degrees, its Y-axis corresponds with the Z-axis of the outside (world) coordinates.
A classic problem in the real world is a telescope, or radar, which must "track" an object that goes directly overhead. Put yourself in the role of either of these devices. Let's assume you're tracking the path of the space shuttle. It first comes into view on tyhe horizon, and your body is facing a certain direction so that you can see it. As rises higher in the sky, your body continues to face the same direction, but your head rotates upward. Once the shuttle passes directly overhead, your body may still be facing the original direction, but now your head is looking straight up. In order to maintain your vision of the shuttle as it continues on its path to the opposite horizon, you must either rotate your body around 180 degrees, or continue to tilt your head back (uncomfortably).
There are ways around this situation (at least for real tracking mechanisms), such as offsetting the axes, but they generally rely on some advance knowledge of what may happen, so that they can avoid gimbal lock. Similar steps can be taken in the modeling and animation world to avoid the situation, but I don't know of anything that can eliminate it altogether. The rule of thumb is to plan ahead.