Think of it this way.   Repeated running through the guides is "knocking loose" the shape of the knot.   Certain knots only hold well when cinched down tight as it is the cinch that "holds".   Other knots its the shape/wrap of the knot that self tightens when pressure is put on it.   

To prevent this we would dress our Bimini twists and spider hitch knots with a little clear nail polish.   Might work good on the braid to leader knot and as a bonus the knot will slide through the guides easier.