Clicking the Knit button will call rmarkdown::render in a background R session.
This means it should be the same if you render in a clean session.
Have you looked inside rebalReport_ok2delete.log ? Is there more information ?
Which latex distribution do you have installed to convert to PDF ?
I can't explain the difference leading to this error for now. Having more information would help.
Upgrading your packages in R (rmarkdown, tinytex, knir) and LaTeX could help.