Per #70, I'm still having this issue. Attached is a zip to help debug:
thuderer-shortcode-issue#77.zip
Just extract, run composer install and then php shortcode.php
The output with each parser can be seen via this online diff: https://www.diffchecker.com/vejLhuQq
Notice, the shortcodes are processed at the bottom of the file for the regular parser, but as things progress upwards, it cuts out.