This issue seems to be similar to what has been found with 'fossil cat',
and subsequently fixed:
http://www.fossil-scm.org/index.html/info/f2fc37c063af9fae

In brief, when the source-code contains CR/LF line-endings, 'fossil diff'
in non-console output (when run non-interactively) on Windows shows extra
empty line for each line of the actual source-code output. Meanwhile all
looks ok when it's executed from the command-line (cmd.exe).

Digging through the fossil guts, it seems to lead to
"printf.c:fossil_puts()"
In this case the output gets generated by fwrite.
printf.c:892
http://fossil-scm.org/index.html/artifact/2de9ca8ea140e35da05eafeb6a447a2fd4069438?txt=1&ln=0

This issue seems to clear by applying the fix similar to how it was done
for the 'fossil cat' case above. Which is switching stdout/stderr mode to
binary prior to fwrite, then restoring it back to text-mode.

Hope this would speed up the fix so it could make it into 1.37. I would've
gladly fixed it myself, but have not mailed yet the Contributor Agreement..
(I have signed it though :)
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