One of my forum users (Taowen) has posted an extensive list of links describing the problems that arise with the Nellymoser codec. It shows quite clearly that a wide variety of users are annoyed and restricted by this issue.
For those who don't know: Nellymoser is the name of the audio codec that is used when you record audio via the Flash Player (and subsequently save it to FCS/FMS). While the codec itself is not a bad one it's extremely restrictive. It's practically impossible to convert the flv audio portion to a portable format (such as mp3) if the Nellymoser codec was used for encoding. To make matters worse the developer has no choice but to use Nellymoser when recording audio through the Flash Player. Standalone encoders such as Sorenson Squeeze on the other hand can use mp3 instead.
Nellymoser does offer a transcoder but it apparently costs thousands of dollars to license. Adobe has promised to deliver a transcoding tool free of charge but this has been held up by legal issues which center around Nellymoser's licensing terms. Adobe needs to take urgent action. This issue is hindering innovation around the Flash Video format, not driving it.
Check out this link list