Ok, I have noticed that this UI problem happens much more often in proportion to the amount of things on my screen. I mean that it won't happen until I have a considerable amount of verts, but the more verts I have the worse the problem. I'm working with Zuri on an age and when I load it into blender and rotate the view, the manipulator handle and everything jump in and out of perspective. This REALLY sucks, because Zuri has done everything in 2.49 and we have to use 2.49 to "publish" the ages to uru.
If 2 ppl on this small forum have the same issue then, this can not be all that uncommon a problem, but when I search google all I find are my own posts in different forums; and now with 2.6 out I know that my chances of ever finding a solution are nill.