Ugh, I had a feeling something like this would happen. FLV isn't supported by quicktime apparently, because it's a terrible video player. It's the most simple file format out of any other file format available and yet somehow it doesn't support it. That just goes to show, just because something is made by a big company, don't ever expect it to be good. (Reminds me of adobe and flash, flash is terrible)
I'll have to put in the other file output plugin which does support other formats as well.
Options for dealing with it:
1.) Get a real video player that isn't totally terrible, such as VLC which is available for the mac supports every format and codec on the planet, and is much more optimal
2.) Convert it to mp4 via a utility:
Here's the best way to convert via the ffmpeg command line utility:
ffmpeg -i myfile.flv -acodec copy -vcodec copy myfile.mp4
3.) Wait until I add other file type output support