I think that it is because the two types of MRI detirmine to color differently. T1 determines color based on spin-lattice relaxation time, while T2 determine color based on spin-spin relation time. Both methods distinguish between water and fat. With T1, water shows up dark and fat shows up light. With T2, water shows up light and fat shows up dark. Since cerebrospinal fluid is mostly water, it shows up dark in T1 and light in T2.