But fully invisible, it's throw TNT.

Are you using the newest version? 1.1.4b beta?
Did you restart the game after disabling the creeper?
Was it a creeper that perhaps already spawned before disabling it?

This bug should be fixed in the latest version afaik. After running various debug tests; the entity never spawns for me when disabling and restarting.

Yes, in 1.1.4b fixed. Thanks!