I've been working on a short animation for a client of mine and one element that comes up later in the animation keeps popping in and out at the very beginning of the timeline. It's Opacity is at 0% so it shouldn't be doing this. I've tried restarting AE, restarting my computer, and completely deleting the element and redoing it. The problem still persists.
Purge all of you cash.
IN addition to purging the cache check your motion blur setting and/ or effects that may introduce artificial time-based blur such as Timewarp. This sometimes happens because in undefined areas at the beginning the dieection is ambiguous....
Motion blur was going to be my first suggestion, too. Turn it off and make a quick test render of the first appearance of the element.
Zoom WAY in on the timeline to see if there aren't maybe a few extra position or opacity keyframes where you least suspect them to be. If you have trimmed the layer, you may have left keyframes off the timeline.