Educated guess would be that maybe you've overtightened the top section of lacing slightly and / or your feet are moving enough in the boot to press against the cuff hard. I can't remember what the lacing configuration is on the Borneo, but it's generally possibly to lace boots so that the forefoot is held snugly, but the top couple of lace hooks are a little looser so there's enough give for comfort around the top of the ankle cuff. Some boots have a locking hook third down from top specifically to do this.
Otherwise you need to use a surgeon's knot or similar to isolate the upper and lower laced areas, if that makes sense.
Sometimes it's simply that the boot simply presses on the wrong part of your ankle, which has happened to me, but usually you can improve things with careful lacing.
