Which set of scale are you using? There fantasy line or scale color, or new warfronts.
I mainly paint with scale75 I haven't seen the issues your are describing about. However max pointed about shaking, and scale paints need extra 5mintues of shaking, like seriously shake them and when you think there ready shake them longer, I really like there paints but they can be pain in the dick. My paints sit for 17-26weeks at time and some time even longer depending how long i am away for work. From sitting that long I have notice they separate faster, than others. With this being said the best way to tell if there full mixed is when you drop them if you see any clear liquid there not mixed enough. Thats the binder, so shake them again.
Some other things could be, what are you thinning them with? For brush work I use water local tap water so unsure of the mineral level and everything else in it. For airbrush work I use there thinner, tho there isnt much difference on thinners. If you sure crazy about not effecting the paint you can invest in gallon of baby water at walmart its like .99cents basically they remove all trace minerals from the water. I know a few painters that do that, as they swear there tap water effects the paints. Possible thinning them to much and the thinner just builds up and acts chipping agent and stripper at the same.
You can always email them, the stateside website is on the slow side to respond but they maybe able to help you. Or try there euro site they may respond faster.