For some reason the mp4's I reencode have very low volume.
ffmpeg -i "\"$FILENAME\"" -sameq -vf "\""movie=/files/logo.png [watermark]; \
[in][watermark] overlay=main_w-overlay_w-10:main_h-overlay_h-10[out]\""" -ac 2 \
-vcodec libx264 -threads 0 -acodec libfaac -async 2 \
"\""$OUTPUT_DIRECTORY/abc$OUTPUTFILENAME"\
I added a few flags to keep the audio in sync, etc.