What is likely happening is that the bar is resting on one of the vertebrae of your neck and thus causing the pain. I would suggest attempting to create a "shelf" with your shoulders and traps. Pull your shoulders back slightly and flex your upperback muscles, this will create a cushion for the bar to sit on and keep it off of your neck. Good luck!
James 1:16-17 ESV
Do not be deceived, my beloved brothers. Every good gift and every perfect gift is from above, coming down from the Father of lights
With God's help...Mens sana in corpore sano