This have been reported before, but thanks for pointing out!
Haven't seen this before, bug I guess your right about possible illegal build by TLG
Has been reported, and from what I understand fixed in LDD4.
Very good find. It's not often these days we get this kind of serious bug. Concider it reported.
I agree it's strange only the jumper plates is removed. But depending in which order you place the parts, if you re-place them many time etc you can get these issue. After playing around some, I managed to get it so other parts also were removed, so it could be a case of the slack that is in LDD doesn't go in your favour on the jumper plate. In any case it's an illegal build that TLG used themeselves (the more I learn about this, the more I see that they use illegal builds when it suits them )
When a brick is removed, LDD creates a file here
C:\Users\[User Name]\AppData\Roaming\LEGO Company
You can open and have a look at it.
If that doesn't help, you can import both the "old" and the "cleaned" file to LDD Manager and analyze for the difference (i.e. the removed bricks)