I had the same problem with a pair of ASOLO hiking boots. I pushed it to the point that I bruised my tendons and had to spend the entire summer hiking in low cut shoes, carrying boots and putting them on only when needed. NOT WORTH IT - you can end up with long term or even permanent damage.

The problem is probably that the back of the boot is "indented" above the heal cup more than your foot / ankle shape will tolerate. A good boot / shoe repair place can stretch this part of the boot, but it may not be enough and it may not be a permanent fix (stretching tends to reverse itself after a while).

I've had a very similar problem with Meindl Borneo's (GTX, B class shoe). I thought it would just go away, but after two days of hiking I could barely walk in those shoes. Had to do the rest of the trip on sandals...

Sollution? A different brand of shoes (first Lowa, now Hanwag), as there was something with the fit of the Meindls that just didn't work for me.