I'm asking my 2nd tier support team to take a closer look at this one. I noticed that if I combine the View search and results into one single shortcode, the term post counts are different. I'll let you know what I find out.
Just a quick update to let you know my 2nd tier team has figured out how to replicate the issue in a clean site, so the problem is reproducible under specific circumstances. We will continue to investigate and keep you updated here.