Hi Hellwalker,
It seems to be a problem that affects only a certain group of people, who try to position elements at run-time ;-)
There is a solution to it posted, e.g. here:
scirra.com/forum/windowwidth-and-windowheight-not-working_topic49092.html
but it's hard to find - and I found it very frustrating for a long time ;-)
In brief:
Create a global variables, e.g. ETWindowHeight, ETWindowWidth. Set them to the WindowHeight and Width as defined at edit time. From then on, use these to position your elements at runtime, rather than original variables.
I think it would be nice if a similar solution was built into the engine - or maybe it is, but I don't know where to find it? ;-)
Cheers,
Greg