It is perfectly possible that some guitars behave in the manner discussed simply because the neck (and maybe, to a lesser degree, the soundboard), are not reacting instantaneously to the change in tension caused by the altered tuning.

It is impossible to say where and why this delayed reaction might occur, but one thing that might be worth trying is loosening the truss-rod,( with the strings fully detuned ) putting some tension on the neck by bringing the guitar up to say, two tones below concert pitch, detuning again and tightening the trussrod to its original tension. This just might get rid off any pent-up stresses in the neck which may be causing the problem.

Murray