The SourceTree diff gets very confused when it has to compare long lines (in my example they are about 5K-10K characters long). In the attached screenshot st_diff_confusion.png, the only diff present in the commit was the replacement of the four lines in red (displayed OK) with four slightly different lines in green, which would normally appear directly underneath the red ones (see the healthy example in st_diff_ok_on_shorter_lines.png). In the case of the screenshot, as you can see, the green lines went somewhere off-screen.

I have also seen an example of the long red lines painting right over other lines of the file, but unfortunately cannot reproduce it in a screenshot now as this was with some intermediate diff I have not committed. I suspect though that the underlying cause is one and the same. Thanks.