Your scales are changing with time, heat from grinding, etc in my opinion, or your surfaces are not flat. Think about it: if you have a perfectly flat surface on the blade handle and the scales, nothing should "lift". Work to get your surfaces flat before gluing. I say this ONLY because it has happened to me as well in the past. If your handle material is indeed lifting, then the scales are changing dimensions as they are heated up. This is a problem for me too with some handle materials....particularly with stag, bone, & wood that has not dried down. I have some materials that I grind on and they naturally get heated up in the grinding process...they will appear flat after grinding, but be warm or hot to the touch...when cooling down they will bow up on me...this could be your problem. When this happens I just let them cool down and take my time flattening them on out...got to force myself to slow down. I have found some woods require a long time to dry out as well.....got some beautiful olive wood from the Blade Show a few years ago...every piece bowed up on me...now I let it "season" for a year before I even work it.
Best of luck!