Seems it’s not working with custom structure. I have similar to Mark’s setup, here’s my root folder:
/.git (Git folder, obviously)
/_ (Git ignored folder with Sublime Text project files etc)
/content (copy of wp-content – languages, themes, plugins, uploads, backups)
/core (original wordpress folder)
.gitignore
index.php
wp-config.php
…
Plugin does NOT report any errors while commiting, it produces empty .sql dump (0 bytes), says that commit was successful but it’s not present it my local Git repo or remote (BitBucket.org).
Everything was tested under Windows 7, Nginx 1.7, PHP 5.5 with OPcache, MariaDB 5.5, Memcached 1.4 (with php5-memcached extension). Exec and Passthru enabled. WordPress 3.9.1. Git 1.8.3.msysgit.0