I am using qgis 2.2 (I have also tried this in qgis 2.0 and arcgis 10 with the same result) (I have some basic understanding of netcdf, but I am probably missing a lot of details...)
I have manged to read in some netcdf-files and have them displayed correctly. Some other fails miserably, as the coordinate infomation is ignored and the file is displayed south- and eastwards from 0,0 ... Is this a known problem? I have been looking at the files with ncdump, but have not been able to spot any differences that should make one of them work and the other to fail. When looking at the metadata in qgis or arcgis, it is clear that a lot is missing for those files that do not display correctly.
Edit: When converting the files from netcdf4 to netcdf3 they worked fine. is this a known issue in arcgis / qgis? (using arcgis 10, it seems to use gdal, but I cannot find which version, qgis 2.2 from osgeo4w using gdal 1.10)
Edit2: The original files were so large it was a bit difficult to share them. Now I have made an example file that behaves the same way: http://sickel.net/div/test.nc - it is created from http://sickel.net/div/test.cdl - it should, as far as I do understand, cover an area from -160 to -15 E, 20 - 60 N ie most of US main land and neary to UK in the atlantic ocean, but it ends up from 0,0 and south and eastwards in qgis, in arcmap 10.0, it ends up as a point on -160,20 ...