Hi Trenton,
Thanks for the video, now I know what you mean.
Appearently the alpha that you used inside of your material doesn't work when you publish the material. I didn't know that either.
However, to solve your problem I would go about and try to put the alpha inside of your scene and not inside of your material.
In your scene you have a Quad called picture which is published so you can change the source in the sequencer, which is perfect.
What I would do is change the Z-POS of that quad to 0.
Then create a new quad and also a new material but define it as a mask. As the source for that mask you use the video which you have used originally in your material itself.
Put the Z-POS for that mask at 1
Finally, position the quad which has the OTS on Z-POS 2. That way the mask only hides the picture and not the OTS itself.
If you want you can also put the material on your timeline if you just want to play back through your timeline instead of using the autostart. This also ensures the sync'ed playback of your animation and the alpha.
If it's not clear, let me know and I'll make a demo for you.
Good luck and merry Christmas!
Kenneth
#XPression