[Andrew Roger]

If the flash component is truly installed, you need to click the little plus tab in the top right corner of the settings window and select Quicktime Export Components. It’ll pop up in your custom settings at the bottom. Click that and move to the browser where you can select FLV as well as many other non-quicktime based formats like WMV, AVI, Dvix, if you have them installed. If you mess with the settings, a non-FCP window will pop up. You’re actually using Adobe’s application under the guise of compressor. Make your settings, drop it on your clip and submit.
Hope that helps!