As I recall, there is an issue with Windows 8 and the offline recording function. Not sure if you are using Windows 8, but it may be worth trying to do it on another computer.
However, before you go down that road, know that the FLV versions of the meeting recordings are notoriously difficult to edit. If you don't need to have the recordings in a different format, I would recommend that you do the following instead (will be much faster overall).
Take the URL for your meeting recording and add /output/YourNameHere.zip?download=zip. You can name the zip file whatever you want. This will pull the recording source files down to your local computer. Next, browse to a desired location in your Content library in Connect and re-upload that zip file. You can name it whatever you want, and even create a custom URL for it. Once it is uploaded you will have a second version of the same recording on your server. Just re-upload that zip file as many times as needed. You can then edit each version of the recording separately, allowing you to create as many versions of the recording as needed.