I have the same problem on a current design, where did you change the constraint values?
can't find it on constraint manager.
I was now able to solve the problem,
i changed the "package_height_min" of the "keepout_top" layer to the actual height of my symbol,
and then changed the "package_height_max" of the "place_bound_top" layer of the symbol to symbol's actual height.
Now, there is no conflict anymore.
contact me if you have further questions