Ok, I have now re-installed the software which went fine. I then installed the MatroskaSplitter and ffdshow as per the instructions. I then analysed a 15 second MOV clip which went fine and it also exported fine using the ffdshow option for the .avi.
Then came the proper test, stabilising a 47 minute clip with a filesize of 3-4GB. The video opened and would play perfectly well in the Mercalli package. The analysis went well and the preview played perfectly on the PC. Now to the important bit, to export the file so that I can use it, no good.
I selected exactly the same options as for the short clip and it just sits there at 0% on the progress bar doing nothing. I opened the task manager and the CPU usage was very low, the machine was barely doing anything, and certainly not rendering a video.
Hope someone at proDAD can suggest where I go from here because I'm damned if I know!