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Only the second watermark is present when using this command line:

ffmpeg -i in.mp4 -loop 1 -i wm1.png -loop 1 -i wm2.png -c:a copy 
-filter_complex "[1:v]fade=in:st=0:d=0.5,fade=out:st=30:d=0.5[watermark1];
[0:v][watermark1]overlay=(main_w-overlay_w)/2:main_h-overlay_h:shortest=1[video1];
[2:v]fade=in:st=30:d=0.5,fade=out:st=60:d=0.5[watermark2];
[video1][watermark2]overlay=(main_w-overlay_w)/2:main_h-overlay_h:shortest=1" out.mp4
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    Please add the full, uncut command line output, and ideally, also a sample image/video to reproduce.
    – slhck
    Commented Aug 5, 2015 at 8:08

1 Answer 1

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You need to add alpha=1 to the fade filters.

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