Front ortho opposite way around to expected I have a box and have drawn with grease pencil 
F on the front (+Y)
B on the back (-Y)
R on the right (+X)
L on the left (-X)
T on the top (+Z)  

Right ortho shows the R
Top ortho shows the T (upside down)
Front ortho shows the B!?  

Is this correct? It's extremely confusing.
You should accept the orientation presented by Blender.  
You should not fight with Blender on this small matter
I think you should switch to each view and then use the grease pencil
I think it is more likely that you can work successfully with Blender on a second try ... rather than you have discovered a flaw in Blender.
You may want to see a tutorial on grease pencil