Okay guys, I've worked with video a loong time. I think the problem here is HDV codec. And here's why. I'll try to make it easy to understand.
When you import footage from a camera directly to the HDV codec, basically it records exactly what the information is from the camera, which means it'll stay exactly that way. So if you imported footage that was interlaced, then it'll be imported interlaced; if you try to play it through Quicktime, it'll show the interlaced lines regardless if you check off deinterlace or not. This is because the codec is decoding compressed information, and doesn't read the information as scanlines. All it does is it decodes the information, and Quicktime displays exactly what the information is, and doesn't natively do post-processing deinterlacing for compressed codecs.
So here's a solution. You need to export that HDV file to a codec that is uncompressed and supports scanlines. Of course this'll yield a very big file. But once that's done, you can re-export that big file and compress it back down to a smaller file size with proper deinterlacing. Here's a list of codecs that support scanlines:
-DVCPRO codecs (I'd probably only try DV/DVCPRO - NTSC)
-Apple ProRes codec (a new codec only on Final Cut Studio 2, although I'm not sure if the latest Quicktime Pro already has the codec compiled in it)
Assuming you have Quicktime Pro to deinterlace, I'll provide some instructions.
Step 1: Open up your HDV file. Go to File > Export. Once the "Save as" window pops up, "Export" should automatically select "Movie to Quicktime Movie". If not, then select this option, and then click on "Options" right next to it. Select "Settings", and select a codec that supports scanlines (I'd go with "DV/DVCPRO - NTSC"). You'll know if it supports scanlines by when you select the codec, and there will be an option to select the "Scan Mode", in which case you can choose interlace or progressive. So, for your interlaced footage, you'd select interlace. Then, you'd go under "Size", and specify the correct resolution. Export with those settings, and after that completes, you can re-export that big file to a compressed codec.
Step 2: When compressing it, open the big file that you just exported, go back to File > Export, click on "Options" (make sure "Movie to Quicktime Movie" is selected). Select a compressed codec under "Settings", such as H.264, and go to "Size" and make sure you check off "Deinterlace Source Video". Export that, and boom, you'll have a playable, compressed, deinterlaced HD source file at the fraction of a file size.
Of course, you'll probably have a hard time understanding this, but if you follow the steps, you'll get a properly deinterlaced video for viewing on a computer.

I'm not expecting anyone to understand all this gibberish, since it's hard to explain all this junk.
