As far as i've researched, this seemed as if it was an error in the firmware. AF functionality is lost as soon as the camera commences record in movie mode. Servo attempts to move but doesn't.
Tests with focus faults
Record in movie mode cycling Shutter/AE lock button modes
Disabled AF during record
Tried all AF modes
Rack focus functions not available (red cross)
Follow focus functions ARE available however when pushing the focus buttons the servo makes noise, but does not move.
Test with Magic Lantern firmware uninstalled All the above tests were successful and got back focus functionality.
My 10 cents to the community for this wonderful project. Thanks to Alex.