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I was able to solve similar issue with col (filter reverse line feeds from input).
col
java -jar my-jar.jar | tee >(col -pb | tee >/tmp/my-jar.log)
EDIT: Refined answer to better match the question.
java -jar my-jar.jar | col -pb | tee /tmp/my-jar.log
java -jar my-jar.jar | tee >(col -pb >/tmp/my-jar.log)
