Ok heres how I fixed it, I took a piece of aluminum foil, folded over a few times, and put it on top of the piece under the ram rod of the hand tool to get the ram rod to go up a few more thousandths.
I occasionally have this problem; the biggest issue is it makes it difficult to measure OAL since the primer adds a few thousandths to the measurement (I measure OAL using a comparator for every LR round I load).