Aha, I got it back.
I'd been playing with the Crop feature on a 360x180 pano image and if you reduce the Pano FOV from 360x180 then the Nadir patch part of the Panorama properties/Picture parameters dialogue disappears because it no longer applies.
I had then resized the crop box to show the full 360x180 but to recover the Nadir patch parts of the dialogue you then also need to click on the pano image in the main panel to refresh the Panorma propreties/Picture parameters dialogue.
Nikon D40, Nikkor 10.5mm fisheye, Sigma 8mm f3.5 fisheye, Nikkor 18-55/50/35mm lenses, Nodal Ninja 5 Lite, Nodal Ninja 4 with R-D16, Agno's MrotatorTCS short.
Nikon P5100, CP5000, CP995, FC-E8, WC-E63,WC-E68, TC-E2, Kaidan Kiwi 995, Bophoto pano bracket, Agno's MrotatorA.
Merlin/Orion robotic pano head + Papywizard on Nokia 770/N800/N810 and Windows 8/XP/2K.