I'm at work now, so I can't give the full explanation but...
Okay, the standing part of the core comes up the rope, it goes through the crossover, through the eye, then it becomes the tapered tail that goes back into the rope.
What is happening is that the standing part of the core (and some other things) are grabbing the tapered tail and pulling the tail down deep with the standing part.
You've figured out that it's wrong.
If you were splicing Double Esterlon or Stable Braid, you could play around with this more to really see why and how it happens.
To fix it- you need to push the slack in the cover all the way over the side OPPOSITE where the tail is getting buried. With the cover bunched firmly pinch the cover so you are grabbing the core (or insert an awl or fid THROUGH the rope locking the cover and core together) then pull the tapered tail out a little. This is "zeroing out the eye."
It can be prevented by keeping tension on the eye while running the splice home.
Make sense?
love
nick
ps- so you know- you are starting your double braid splicing with one of the hardest-to-splice polyester double braids known to arborists. It only gets easier after this!