Thank you for your reply!
We've tested a bit more, and I have to admit, the description I gave was a bit overly simplistic (I've included the details now in the full description.
To be precise, skeletons start to have random behavior and don't flee anymore at around Y 140 in the nether. We've made a video to show the bug more precisely.
EDIT: We've just found out that this is not only true in the nether, but also in the overworld on Y 140+ Coordinates
UPDATE (solution confirmation for an unmodded multiplayer server)
My example:
I was catching fire only when returning to the Nether from the Overwold. My Overworld portal (5x5 sized portal) bottom center block is at [710, 25, 431]. I went to [710, 25, 431] in the Nether (not the Nether equivalent coordinates). This was in the middle of a lava lake. I filled a portal sized area at those coordinates, plus some surrounding area with a solid block (approx. a 7x7x9 area filled).
This HAS solved the problem for this portal. After doing this, I did not have to move EITHER portal, and the portal behavior is now normal in both directions.
In my case I am not sure which part fixed the portal:
A) Because the chunks at that location [710, 25, 431] had not been generated in my world in the Nether?
B) Because I removed the lava from that location and the surrounding area?
Also confirmed in 1.11.2. I have confirmed with spectator mode that there are no lava blocks in the vacinity of either portal.
Confirmed in 1.11.2.
Happening on a vanilla pc server 1.11.2 with minecarts. I have removed all minecarts and minecart items from loaded chunks. The warning messages still appear.
Can I get this reopened please. The mods response is not a response.
Not a mod, but as far as I know, it is because the second item gets burned by the lava. When two items are dropped, one is collected instantly while the other is laying for a short amount of time on the ground, enough for it to be burned by the lava. I remember ilmango explaining this occurrence in his videos once (panda slime farm in the peaceful series, iirc).