Compressing video for Flash

Hello. I have a group of short movies shot for the web. Since I upgraded to the latest version of Compressor, I have had problems encoding the movies (made in FCP7), for delivery to Flash. When I bring them into Flash, it says that it 'doesn't recognize the format blah blah blah, although the videos might have been created for use on web or devices'.
I tried making the videos .mov (this was the ideal format, as I seemed to be able to achieve the most efficient compression that way). I also tried encoding them as .mp4, but Flash still rejected them. I am at at total loss. The worst part is now I am, at least temporarily forced to use Adobe Media Encoder, and the file size is much larger and the quality is nowhere close to what I'm getting out of compressor. I'm sure that I'm probably missing something here, as I am relatively new to compressor, but I do know the program well enough to try all the obvious options.
Any suggestions/tips for encoding movies in the latest version of Compressor for use in Flash?

I guess I'm really trying to find out how Compressor encodes for Flash properly. I just get so much
better quality and smaller files with Compressor.
"BETTER QUALITY" is rarely objective. There are too many tradeoffs in bitrate, frame rate, frame size, codec tweaks, and multiple pass encoding runs. Flash is a wrapper, like Quicktime, sort of, and there are several true Flash encoders that use wildly different true Flash codecs and compression algorithms.
Google and versiontracker both returned about 15 different products for the Mac and dozens for PC including some cards. Some are cheap.
http://www.sothinkmedia.com/flash-video-encoder/
http://www.video-to-flash-encoder.com/
http://www.freedownloadscenter.com/Best/flash-encoder.html
http://www.geovid.com/Flashto_Video_EncoderPRO
http://www.kibisis.com/kibisis/index.asp/
http://www.ustream.tv/higher-quality
http://flash-video-encoder1.software.informer.com/
http://download.cnet.com/Wondershare-Video-to-Flash-Encoder/3000-2194_4-10473277 .html
Here's an obsolete Flash encoder comparison chart:
http://www.mediacollege.com/adobe/flash/video/encoders/
bogiesan

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