I don’t think you should compare the COM Pull En. output with the work of the pulling potential. If they are “almost the same” but one with negative value, I would think it might be more of a coincidence. Does What does "COM-pull-energy" mean in the pulling process help?
Otherwise, could you post your COM Pull En. plot (and the output from gmx energy) along with the pullx.xvg plot and the value of the constant force you are pulling with?