First check your HDD carriers/sleds are all the same size - MacPro1,1 to 3,1 use a smaller in length sled. MacPro4,1 and 5,1 use a longer one since the SATA ports are on the backplane itself while the earlier models are on the case.
Second, check if where the SATA ports are screwed to the Mac Pro case are not bent, very common to happen with used Mac Pros from people without much care.