I seem to have great difficulty using the geoprocessing tools in QGIS. Sometimes they work fine, sometime no matter what I do I get a null result, even though I can see I should be getting a selection. I am mostly using overlap and clip, and I have made sure the two (polygon) shapefiles use the same CRS and that if a selection is used that it overlaps.
I must make it clear that this does seem to be an intermittent problem, but restarts don't cure it.
Is there anything else I should be looking for?