The "captures two of everything" problem is usually due to one of two things. First, do you have a conversion setting active? A download followed by an automatic conversion can sometimes appear as though two downloads were happening. If you are getting "two of everything" on sites other than YouTube, then this is likely the case.
Youtube has been constantly changing the way they are streaming their media. With this latest update, the recommended YouTube download method in Replay Media Capture is Raw (see Settings->Internet->HTTP Adv). If the quality is changed on the YouTube video, a new file will be downloaded with the new video quality setting. The newer YouTube delivery method is "adaptive". As YouTube determines that there is sufficient bandwidth, they might start streaming another video with higher quality audio. Consequently, a second or third download *might* start with different audio bitrates. Typically, the largest final file size will have the best quality audio. If you try canceling one of the "extra" video downloads, it might be re-queued. If you don’t want the extra downloads, stop monitoring after the video is initially captured.