If you feet are this mismatch I would assume you would know by now. If you don't regularly have this problem with shoes, then the most likely cause is manufacturing variance. I think you have a defective shoe and should exchange them. If that doesn't solve the problem then you can look at stretching the shoe.

Gortex is still flexible, so I would assume you could get some relief to your problem by stretching it. People stretch out hockey skates and those are much more stiff than your hiking boot. I would still only do it if this is a known issue with your foot. Otherwise it is a defective shoe.