The current version displays images in neurological convention (left on left). I have submitted an enhancement request for radiological convention (left anatomy on right side of image). 
 https://github.com/neurolabusc/MRIcroGL/issues/12
As I understand it, the radiological convention assumes one is viewing axial slices above the head and coronal slices from behind the head. While radiological convention assumes you are looking at axial slices from the feet, and coronal slices from in front of the individual. Therefore, the images are not actually flipped, and the 3D renderings are identical for radiological and neurological convention. It is a little tricky to implement as we need to ensure that the drawings created by the user are saved/loaded correctly, that the MNI coordinates do not change (left is always negative), etc. In the meantime, if you download the MacOS version of MRIcroGL you will see that it contains the companion program MRIcro which does provide the option to view in radiological convention (Preferences, "2D Radiological View" checkbox).

-c