It seems to only affect spawners that I found in creative before returning in the survival world. Seems so weird that two seperate worlds though identical, would affect each other. I did create the creative world by copying the survival world.
The first seed was: -1946794855 with Wild Update, Vanilla Experiments, and Custom Biomes experiments turn on. At coordinates 61 -24 -674.
The second was seed: 2082270357 with no experiments, at coordinates 340 -50 530
I am also having this problem. I jump out of a boat, it is gone! I put down another boat, go a little distance (maybe out of the chunk, I didn't check), when I return, the boat has reappeared.
May be resolved? I was able to mount and tame horses in two different worlds today.