Get new boots. The Vans Encore are similar to the DC Scouts which I had with the single boa. I think the issue is because placement of the eyelets/lace crossover for the cables are more centralized at the top of the ankle and pressure is not well distributed at the top of the foot to get a proper lockdown. So you tend to get pinch points around the ankles and any further tightening of the boa makes it worse. Look at the Ride Jackson single boa and you'll notice an extra set of eyelets/crossover at the top of the boot to better distribute tightening (at least last season's model was). Needless to say, I'm not a big fan of single boa coilers used to tighten the whole boot since they tend to only tighten the ankle and top.
Some people have tried tightening while in a forward lean position, you might want to try that and see if that helps. I usually do that as well on my dual boa K2 boots.
2011 Never Summer Heritage 158 :: 2011 Rome Targa :: 2012 Bataleon Disaster :: 2012 Flux RK30 :: 2011 Nike Kaiju