The Create CvP files option is greyed out in the Quartus® II software Convert Programming File utility until a Configuration via Protocol (CvP) enabled input file to convert is added.
In the Input files to convert section at the bottom of the Convert Programming Files utility, select SOF Data, and click Add File to add your CvP enabled compiled project .sof.
You will then be able to select and enable Create CvP files (Auto-generated output_file.periph.pof and output_file.core.rbf).
This problem has been fixed in the Quartus® II software version 12.1.1 and onwards.