You must use cable select for all the drives, on both ribbons, or don't use it at all.
I for one have never been able to get it to work correctly with more than a couple of drives.
Cable select is useless (was useless any way in my book, I have upgraded to all SATA devices now though)
So, here are the non-cable select basics: (which usually will get everything working)
1 drive on a ribbon, it must be on the last connection of the ribbon and set to Master.
2 drives on the ribbon, drive hooked to the end of the ribbon must be set to master, drive hooked to the middle connection must be set to slave.
Make certain the cable is orientated correctly, some don't have the tab or notch and will plug in either way, in which case the side of the ribbon with the red stripe is always plugged in with the red stripe towards pin #1 on the device, or motherboard.