When both The Aether and Quark are installed, it doesn't seem to like switching the skyboxes very well if at all, as you can see in the screenshot below (it's showing the overworld skybox):

As stated in my previous issue, only BP, The Aether, and Quark are installed. (and their necessary dependencies, of course)

So, does it not switch them at all or does it sometimes switch them?
Is the sky the correct one when looking through the portal and only breaks when switching or is it broken from the start?
Does this also happen without Quark but with its dependencies?

Also, please try BP 0.3.x (likely won't make any difference, just to be sure).

I am having trouble reproducing the issue with just these mods isolated. Even on a fresh install with just the Aether installed, the normal pinkish-purple skybox won't show. The first time I had encountered the issue with BP, it kept flickering between the two skyboxes while near the portal in the Aether, but I haven't been able to get the normal Aether skybox back since. I don't even know whether to blame Quark anymore. It may just be an Aether issue, I noticed on this fresh install that the Biome was Plains everywhere in the dimension rather than the Aether Highlands except for some random tiny spots. For reference as to the color it should be, here's a picture I found off Google Images: