I've seen this type of question a few times and have tried all the different suggestions but no luck.
I have 2 layers, one polygon and one line. I want to keep the lines based on a selected polygon. I'm using the clip tool under Vector/Geoprocessing Tools/Clip. Each time, when I try to clip when setting it up and clicking OK it goes to 100% within a second or so, then the OK button stays grey for a few minutes. Eventually it comes back asking me to set the CRS for the layer but once done the layer is empty.
This is the area I'm trying to use when doing the clip. The projection for everything is NZGD2000.
I don't know if I'm doing something wrong, if the files are the problem or if there is a problem with QGIS. The files can be found at: