Your efficiency doesn't really have anything to do with the boil. The efficiency is how "efficient" you are at converting and then washing out the sugars from the mash. Boiling is done after that process so it has no bearing on efficiency.
Also... like northern was saying... gravity is linear and fixed.
Gravity is simply the amount of sugar that is desolved in the solution. You can't get more or less sugar into a boiling pot unless you specifically add sugar, or replace the boiling wort with a lower gravity wort... or water. I am guessing you don't have a leaking pot or something wierd so it is probably safe to assume the amount of sugar in your boil pot isn't changing.
What WILL change is obviously the concentration of sugar since, by boiling, you are removing water... making the sugar more concentrated... and increasing gravity.
So, after you boil all of that down (pun intended) I think the real question is: How do you go from 6.5 gallons of 1.046 down to 5 gallons of 1.050? On the burner... the speed with which you boil has nothing to do with it. If you go from 6.5 down to 5 in ten minutes or ten hours, the effect is still the same.... all you've done is take out a gallon and a half of water. Sugar won't evaporate so you can't lose sugar that way.
... and 6.5 gallons of 1.046 CAN'T turn into 5 gallons of 1.050... unless you take out some of that boiling wort (and sugar) and add water or something.
6.5 gallons of 1.046 down to 5 gallons will give you 1.060
I can't think of anything other than the gravity readings are wrong.
First, Do you know what temp your hydro is calibrated to? Most are 60 (that might be a SMALL factor)
Second, you said you measured a 1.046 preboil and then had 1.014 second runnings... are you making sure ALL of the second runnings are run off into the kettle and then mixing it all REALLY well... then chilling your pre-boil down to 60-something degrees before taking your pre-boil gravity reading? This is my guess for the problem. My guess is that you're pre-boil wasn't actually 1.046 but after a really good mixing with the last of the second runnings and then a chilling down to room temp, your pre-boil was more like 1.039... which would give you a 1.050 post-boil.