OK, more on the problem.
First off I got After Effects to open after one crash after one crash (you can see the crash log in TXT form here). I re-opened the project, which was created via dynamic link from a sequence in Premiere Pro, though has since been relinked to the the ProRES footage I created. I tried re-starting the Warp Stabilizer analysis, and again it just gave me initializing.
And the blue was frozen on the image:
I checked Activity Monitor and 2 Adobe Processes are not responding, The Adobe QT32 Server and the aeselflink.
And after a minute I got the following error message:
Strangely when I try Warp Stabilizer in Premiere Pro it processes in less than a minute per clip, working just fine in the background, but it does not work at all in After Effects.
I have run permission repairs with both Disk Utility and Onyx, with a full user permissions reset, but that did nothing. Nor did using Onyx to run the daily, weekly and monthly scripts and cleaning out the Caches.
I am going to post on the Adobe Forums now, and see if I can get any help there. This is really frustrating!