I have run into the same problem with the free version of WP Migrate DB. It seems to break when trying to run queries in the process_chunk() function inside wpmdb.php. The specific query that my install seems to have problems with is SET sql_mode='NO_AUTO_VALUE_ON_ZERO';, however there are no WP errors thrown and I don't see anything relevant in the apache logs.
Wordpress 4.4.2
WP Migrate DB v0.7.2
WP Security Audit Log v2.3.3