Adobe Media Encoder: Quicktime H.264 Problem

I'm trying to output my video using QT H.264, and whenever it processes through the media encoder, it gets stuck with the status "encoding", with the elapsed queue time frozen at about :13 seconds.
I've tried using different settings, but I get the same issue every time.
When I encode using a different QT codec (DV/DVCPRO- NTSC, etc.), it works no problem.
My machine is dual-quad with 16GB of memory, so I'm pretty sure it's not my system. The video is only a couple minutes long, so there's not a whole lot of video to process.
Does anyone know a work around to this problem?
Thanks,
Anders

Anders,
I have to make sure we are talking about the same thing. In the Effects Control Panel, you twirled open the Opacity intrinsic effect and clicked on the stopwatch to create a keyframe, correct?
I ask this because you can also adjust the Opacity by using the clip's opacity "rubber band" in the timeline, but no keyframes get added there unless you use the Pen tool or a modifier key in combination with the selection tool.
For the workaround to fix the issue, a keyframe has to be created.
-Jeff
PS - You're welcome. :)

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