Here is an example of what can happen:
After some time figuring out the problem, I came to following conclusion:
If you have a sector with deep water, faked by using the transfer_heights method, and have a stacked sector directly next to the deep-water sector, it will definitely cause problems.
You can put an additional sector in between the portal and the deep water and the proble is gone!
I could imagine this is just another limitation of the stacked sector feature, but it works fine in Zdoom on the other hand.
I've included a little example wad to show the problem:
Edit:
i forgot to mention, that the visual anomalys only appear, as long as you are below the fake floor!
