Actually you would want to set the jumpers to cable select. I have worked with several brands of these adapters and that is what has always worked for me. I have had this exact same problem when trying to manually set the jumper config and it seems to just go away when you set it to cable select.

All of this is of course assuming that you are using a relatively standard HDD on a windows based system. Not being super familiar with Linux and the way it addresses hardware I could not tell you for certain there. More details would be VERY helpful.