The syntax looks right to me. Use single quotes so you don't have to escape the expression:
ffmpeg -i input.mp4 -i watermark.png -filter_complex \
"[0:v][1:v] overlay=10:10:enable='between(t,1,2)'" output.mp4
If you don't have an enable
option, make sure you use an ffmpeg version 2.0 or higher. Timeline editing is only supported there (see Changelog).
If you want multiple images overlaid, use something like this:
ffmpeg -i input.mp4 -i watermark.png -i watermark2.png -filter_complex \
"[0:v][1:v] overlay=10:10:enable='between(t,1,2)' [tmp]; [tmp][2:v] overlay=20:20:enable='between(t,2,3)'" output.mp4
Next time when asking questions about ffmpeg, please include the full, uncut command line output as well. – slhck – 2014-02-10T07:44:14.350