Just to go with what Sargas mentions, all of the disappearing sprites and invisible sprites are all ones created in the game, not present from the beginning. So that would be why is seems to only effect the spawning monsters (not sure if it effects other spawning items, I have yet to notice this).
Though not all of the instances of spawning come after wait times. I am actually not entirely sure what event I have that spawns anything after a wait period. Most of my spawn events are just spawning a creature every random number of seconds. As I mentioned, I never seen that error before or since that one time.
Most of the times when I see monsters disappear or turn invisible, they come from the spawn events as mentioned above. Sometimes when I kill a monster or deploy a landmine or pick up an item (or any action that 'destroys' something) *all* spawned monsters instantly are 'destroyed'. I mentioned earlier that this can be reproduced somewhat easy, though not reliably, by letting multiple monsters wander onto screen and just shoot them. It seems to not work as much when there are a lot of monsters for some reason, but still, its random.
And this happens in both the exported version and the non-exported version straight from the editor.