Not sure that I am qualified to help here, but here goes. You would know th efront and back circuits are separate and so can be bled separately. The equalisation valve may need to be reset in the middle but I would think should not cause your symptom. I would be looking to see if there is any air in the lines when you bleed them. The pedal will go down obviously if there is air or else if the master cylinder is leaking internally but cannot think of any other reason.
Did you rebuild or work on the master cylinder? Is the fluid level changing in either circuit when the problem occurs?
Just thoughts.
Rgds
Sean