You are using a CS cable. Pin #28 is the sensing wire that chooses the drive to be addressed. If a drive sees this signal as grounded, it's the master, but if it floats (unconnected), it is the slave (when pinned to use CS). So on the ribbon cable, one connector will have pin #28 connected (grounded at the computer), the other connector pin #28 just floats. Normally, the far end connector has pin #28 grounded making the last drive on the cable Master, so if only one drive is present, plug it into the last connector.
If you actually set the drive jumpers to Master or Slave, they will ignore pin #28 and obey the drive selector pins and be what you make them.
You should assign the Master/Slave designation of the drive rather than CS if only one drive is present just to avoid a conflict if the cable was made backwards (first drive pin #28 grounded instead of the end connector).