Let me make sure I have this straight.

You have some animated tiles (speed 0) that go solid, blank, solid/blank. [] [] or [] .
You place some in the level, some of them get Destruct Scenery events. But when the ones with destruct scenery get shot, the ones without disappear.
If you put destruct scenery on all of them, they disappear. I'm not sure when they disappear, as you didn't specify.

When do the previously non-ready ones that now have destruct scenery events disappear?
What speed are the animations?
Are you sure all of them are animated? You can set a high speed to the animation to check this.
Does this happen in Multiplayer, or just in Single Player? (You said it originally did, but does it when all the blocks have destruct scenery?)
Do you have any theories to why this happens?
Is the "Battle, CTF or Treasure Hunt" checkbox checked?