I do have a problem though. I have Marked 2.5.35 (978) via Setapp on a Macbook Pro (late-2013) running Mojave. I just downloaded the trial from your web site but the problem is the same.
Here's a very silly bit of Markdown to show the problem:
#Heading 1 ##Heading 2 What a test setup [@Reed:1861aa, 123]
Using Pandoc, I'd expect the citation to appear at the end in the Reference Section, but it doesn't - well not at first sight.
The top half of the attachment shows the Markdown correctly but the citation hasn't been handled as I want. When I toggle the custom processor, as per the lower half, the citation gets done properly but everything else is wrong.
The custom processor path is /usr/local/bin/pandoc and the args are -f markdown -t html5 -s --filter pandoc-citeproc --bibliography /users/mickreed/Documents/Dropbox/BiBTex_Files/MJR.bib