I have several different types of media in my project, but mostly .mov. Some of them contain alpha channels.
As you probably know, .mov is simply a wrapper format -- quite a few different types of video use the .mov extension, though their properties are quite different. So can you please right click on one of them in the VS timeline or library window (or more if they are from different sources) and copy ALL its Properties here or take a screen grab of the Properties box and upload it here as an Attachment.
I suspect, though, that the alpha channel videos might be the culprit. While I can't say with total certainty, I believe VS cannot handle them, and it certainly can't render new video with alpha channel. I suspect that only professional-end products like Adobe Premiere or Apple Final Cut Pro can do so -- though I understand producing alpha channels using the new WebM format is becoming more common -- though still not in VS. It would be interesting, however, if you could also give us the full Properties for one of the alpha channel clips...
So overall, I don't think this is a bug in VS -- it's just something VS was not designed to do.
As ever, though, I will be more than happy to be proved wrong.