MatterControl essentially just prevents the nozzle from traveling below 0 on the Z axis, however is superseded by the printer's firmware as to whether or not travel below 0 is even possible.
Despite the fact that I have it set to 5mm above stop
What is "it"?
Can you run the Software Print Leveling wizard and post the Terminal Log after you run into this problem? http://wiki.mattercontrol.com/Send_Debugging_Information#Print_Log_.2F_Terminal_Log
Please use Dropbox, Google Drive, or a similar service to share the files and post the link in your reply.