If you're getting unexpected results with autopilot coupled ILS approaches, read this tip from FS9 Learning Center;

Intercepting the glide slope

In order for the autopilot to capture a glide slope, you must intercept it from below. Although some real-world autopilots can capture a glide slope from above, standard operating procedure is to intercept and capture glide slopes from below. Thus, many real-world autopilots— and all Flight Simulator autopilots—can only capture a glide slope from below. If you want to intercept a glide slope from above, descend through it, level off, and push the APR button twice to disengage and reset approach mode. Then intercept and capture the glide slope from below.

Try it!