I have two layers, one point file and one polygon. The point file is in WGS 84 and polygon in NAD83-UTM10. The project CRS is NAD83-UTM10. They project fine with on-the-fly projection turned on.
I want to clip the point file with the polygon and understand that all layers need to be in the same CRS to enable clipping or other ftools functions. When I change the CRS of either layer to the other (changing the point file to NAD83 for example), it projects far away from where it was (ie. doesn't line up). This is the same if I right-click to change the CRS or if I "save as." Same no matter which CRS I select.
I'm running QGIS 2.0.1 Dufour on Mac.