After accidentally syncing both the Upright Mode and the Upright Transforms (instead of just the mode) from 1 photo to approximately 200 other photos, I noticed something quite strange.
When selecting the 'Auto' upright mode on any of the other pictures, the transformation was done using data from the original photo.
When realising that I'd synced that transformation data across to a load of photos that it didn't apply to, I tried pressing the 'Reanalyze' button. This seems to have no effect - the images are still incorrectly transformed.
The only solution was to manually reset every synced photo to its imported state (although I suppose I could have undone the sync operation, but I only realised this after doing other changes). After doing this, the transformations work correctly.
Perhaps I have misunderstood what the button does, but if I have, then I can't see how you are meant to resolve this problem