I'm having the same problem with my data set. I had converted raster data from USGS GAP data into polygons and I was clipping buffered polylines from the layers. Everything was working fine until I went to clip another polyline and then I got the zero output warning. As far as I know everything is set to WGS 1984(the data frame, datum, coordinate system). I tried merging all the polygons into a single polygon but I still have a zero output. I tried turning off the background geoprocessing and disabled the Windows Indexing Service but that did not work either. Everything else said to check the Extent environments to see if everything looks right. I do not have a lot of experience so I'm not sure what to look for but I have a feeling that my problem lies there. It's unusual that everything would be working fine for days, carrying out the same processing, and then suddenly not work. I'm hoping someone can give me some guidance, thanks again.