I would check your training manuals, Wizofoz for the reference which states that Boeing recommends manual flight with A/T during takeoff and climb out only. There have been more than a few SBs on the A/T system for the Classic as well.
I have been told that aircraft energy management is the reason behind the recommendation. The A/T system is designed to work in concert with the CMD functions of the A/P. Manual pitch changes can lead to an undesirable (high) energy state during landing when A/T is engaged, particularly during gusting conditions.
You can also end up needle chasing (airspeed) when you get out of sync with the A/T control loop and a sort of hysteresis can occur, a condition that is extremely rare with the A/P engaged.