This is Wick from Media 100. We think we know what you're seeing and what to do about it.
When you acquire to Media 100 (current products) in the DV codec, the application enables a QuickTime setting called "High Quality" on the DV Stream in the background. This gives you a sharper picture inside the Media 100 application. However, when you play the source files you acquired in QT Player or when you export those clips from M100 and play them in QT Player (or any other QT savvy application) you may see some "lines" in the video depending on the nature of the image.
The first place I saw it was a static shot where a door opens. The vertical lines of the door frame look fine, but the edge of the moving door looks "zippery". Turning off "High Quality" using QuickTime Pro makes the problem go away but it also lowers the image quality, obviously. To further illustrate the issue, turning ON "High Quality" for media captured with FCP or iMovie makes the problem appear. Apparently, FCP and iMovie capture DV with HQ turned OFF to avoid this problem. Either way, it's a trade off. We decided to go with the better image quality.
So, what can you do about it? Here are your options:
1 - If you aren't going to export to another application, you can just ignore it.
2 - You can use QTPro to turn off High Quality, but the image quality will suffer.
3 - You can capture to another codec such as Media 100i or Media 100 HD (remember, M100HD can be used at SD frame size).
Option 3 is probably the best choice for most situations. Even if you want to send the video back to DV tape via FireWire, you just need to ensure that DV is the chosen codec in Project Settings>Codecs>SD.