I've used Flash to convert videos to FLV all the time, unless you're using an unsupported option, but I think the ones you mentioned are supported. However, a kicking software I've used for this is Sorenson Squeeze, pricey, but worth every penny if you'll be working with compression of video.
really? i'm using CS3, and i've tried looking in Publish settings, and I've tried doing export. and none of them seem to have any type of FLV option.
In Flash 8, there was a separate video conversion utility in the programs menu from the "start" button in Windows, which did a nice job. Look for Macromedia Flash Video Encoder. Unless Adobe changed that for CS3 which wouldn't surprise me, they tend to take everything useful and replace it with crap that works haphazardly.