Ok that explains it!
Well, first problem solved. If you connect only one microphone you meed to set it up in mono. Other more sophisticated recorders may have a "Pan" control for each channel, which you sould set to centre in that case.
Now, microphones. A stereo microphone is actually two microphones, not one. I imagine it has a mini jack connection wired to the two microphone elements.
I imagine you are using a mini jack to XLR adapter to connect to the recorder. The trouble is, the XLR input channel is a balanced input (two wires plus ground per channel) while the mini hack has two unbalanced channels.
So: you need an adapter for a streo microphone, from a mini jack to two XLR connectors so that you use both recorder channels with the stereo microphone.
What stereo microphone are you using?