I have found a way to use Grease Cut reliably with Blender 2.79
Like many others here I could not use the Grease Cut tool with 2.79, the cut worked but I had to remove the other half manually.
For some weird reason, when I rotate the model in edit mode on the Y axis by -90 degrees, and then rotate it by 90 degrees in object mode (for a total of 0 degrees on the Y axis), it then works for any base mesh.
You still have to select the "Object" option in Grease Pencil Layers, and now use the Z axis for symmetry.
I am using Blender nightly build blender-2.79.0-git.e045fe53f1b0-windows64 with the modified version of the add-on provided by Kent.
Hope it helps someone!