I've noticed if I put the logo sfilter in with the background mosaic, the logo will be blocked out by the video that's playing.
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new background broadcast enabled
setup background input fake:
setup background option logo-file=logo.png
setup background output '#transcode{sfilter=mosaic:logo,vcodec=DIV3,vb=128,scale=1,acodec=mpga,ab=64}:bridge-in{delay=300,id-offset=100}:standard{access=http,mux=ts,dst=0.0.0.0:8080}'
new show1 broadcast
setup show1 input file.mov
setup show1 output #duplicate{dst=mosaic-bridge{id=show1},select=video,dst=bridge-out{id=1},select=audio}
setup show1 enabled loop
control background play
control show1 play