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oooooo... this is where the happy dream of the commandline tools often breaks down (some things are really straightforward, and then you try to go one step further, and you drop off a cliff...) it seems you can't use shuffle with the "multi-file" (still image import) option... in fact, as you may have discovered, mplayer/mencoder is quite picky about things (like that all the images should be the same size / format and already resized to "movie" friendly dimensions. As with a lot of these kinds of tools, you end up using a whole collection of tools together to compensate for what each can and can't do.

For instance, I have a small script (written in the Python language) that could help you out -- it uses another program (ImageMagick) to resize images to a constant size -- and copies the new images to a new folder (& it can also shuffle the order it does this in) -- then it uses mencoder just for the last step to bring the frames together in a movie. If you like I could help you getting this working (installing ImageMagick is a little weird, very do-able, but it asks that you make some small changes to some text files to get it all working.

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