Hi Sheryl,
Adobe Flash Encoder only produces .flv files. Flash itself, makes the .swf file. Previously, (Presuming you have Flash 8/CS3/CS4) you were probably working in Flash and used the "Import Video" menu, which calls Media Encoder. Flash also creates one or two additional SWF files (The player) and a template html file, which need to be uploaded to your final site.
If you have the player swf configured for the correct size, along with the html page, you can use Adobe Media Encoder to create the .fla file, and simply plug the .flv into your site. However, .flv files are not intended to play standalone, like .mov or .wmv files.
On2 Flix will create the .swf and html files for you if you ask it to.
Also, since the release of Flash player 10, you can use standard h.264 .mov files directly from FCP without the need for further re-encoding, so long as you have the player .swf and web .html. H.264 generally produces better video vs. bandwidth, but can't provide alpha channel.
Example of using FCP encoding for flash video at varying bandwidth rates:
www.hd-vo.com
Travis
VoiceOver Guy and Entertainment Technology Enthusiast
[
www.VOTalent.com]