I'm seeing the same problem to Clip or Intersection tool - QGIS giving empty files trying to use the Clip tool since upgrading to QGIS 2.4.0, but have not been able to fix the problem based on the responses there. I tried creating a simple example to ensure was not my data but am seeing the same problem.
I have a series of points & a polygon. I want to retain those points within the polygon only. 
I use Vector -> Geoprocessing Tools -> Clip
This results in an empty attribute table.
Options I've tried:
- I have tried switching the Input and Clip layer in case I had these round the wrong way
- Disable on the fly reprojections (confirmed the layers do overlap, they are in the same projection)
- Checked through Properties to confirm both layers have CRS EPSG:4326 - WGS 84
- I left this simple example running for approximately 40 minutes with no change in outcome in case I was just not leaving enough time (in previous versions this was successful in a short time span).
- I have tried using other Geoprocessing tools to see if it is just clip - I do not receive any output with any of them.
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