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I think I've found my own answer! I'd resized the photos before passing them into CleVR Stitcher. This lead to the app freezing at 90%...
I've just tried it again with the original photos (and I also shut down every other AIR app I had running!), and I've had partial success...
I'm now able to create a stitch, but they are resizing too small to be uploaded! Argh!