I guess that it might be due to the fact that when we tweeze or wax, as we remove hair from the root, sometimes we cause some minor damage to the surrounding skin... and that in turn causes an inflammation response... it is basically like if you had gotten a small wound in that area, and it usually takes for the skin and tissues quite a while to fully recover... but as this same area is irritated over and over again each time you epilate or shave, those marks and that inflammation take longer to go away.
Something similar to what you are telling us about happened to me last year (or the year before) and I remember that as long as I kept on shaving and epilating (which I had to!) the skin would not really get back to "normal" (as in "before" any irritation took place) BUT I remember that when winter came along and that I stopped epilating for some months (I always do epilate often because I swim, but that winter I was too busy to go swimming, I had no boyfriend nor had any reason to "shave" or epilate, so I gave my skin there a "rest"), then, when Spring came along, my skin looked brand new and I had no more spots of any kind in the area.