AME auto-ejecting drives during encoding.

I am running the current version of AME CS6 on an 21.5-inch iMac, Mid 2011 (ver. 10.11.6). I am recording media with a BlackMagic HyperDeck SSD 4K on to OWC Pro 6G Mercury Extreme SSDs (both 480g and 1tb drives). I am connecting the drives to the iMac using the BlackMagic Multi Dock 2 (connected via Thunderbolt). I am having an issue where I set up an encoding queue (anywhere from 2-20 files) and start encoding. The first file encodes well but upon reaching 100% the program freezes and does not move on to the next file. After about 5-10 minutes one of two things happens. Either AME moves to the next file and begins the encoding process as it should, or the program stays frozen and the iMac sends the error "Disk Not Ejected Properly". I have tried using a different external drive dock (A single drive dock made by Rosewill, connected via USB 3.0) but the same problem has occurred making me think that the problem is with AME. This problem can occur when encoding only 1 file, although the encode is successful despite the disk ejection. Any thoughts? Also is there more information that I can give to shed light on this issue?