I decided to try again creating the skybox in the same map(without modifying any of the skybox files) just like i did previously and it randomly just decides to work this time.
the only noticable thing I did was changing the grid size to 8 before creating the skybox material but I'm sure I did that in my previous tries too and I tried making the skybox again with grid siize 2 and it was still working.
I guess it really just randomly started to work
No nothing in DR is random, the cause was obviously a geometry leak, when you have a leak and the point file, red line, points to some place that seems to be fine, then it means one of two things, or some entity has its origin on the void or the hole is really tiny and you can't see it, one way to prevent this small holes is to make the brush's that will seal the void at level 8 like you discovered, one way to solve really small leaks is to select all world brush's (no need to select entities for this) bring the grid size to the lowest value 0.125, and click on "snap selection to grid", that way you solve any hole without the geometry moving away from place.
Btw from my experience very thin brush's can also cause light leaking, this means a light in one room shining into the adjacent room through the wall.
Edited by HMart, 22 March 2018 - 04:11 PM.