What's wrong with Compressor?
 

I did some transcoding tests recently and found strange results when using Apple's Compressor 2 to transcode HDV video to other HD formats. Basically using Final Cut (or any other program) to transcode works much better.

Here's the test:
http://video.terpstar.com/extra/Compressor/

Anyone know what's going on here?

Have you done the upgrades?
 

I don't know if you've updated compressor but one of the errors the out of the box version had was reversing frame order. It was seeing incorrectly the original interlacing pattern in your original footage. HDV is upper (or at least my FX1 HDV is upper.) You can do the update and that will fix the bug or you can just manually make sure the setting is correct. When you select a compressor preset the first tab showing in the inspector shows you the frame rate, aspect ratio, and interlacing order. Make sure the interlacing setting is the same as your source footage.

No, this is something different than field order.

Should this have been posted in Final Cut for HD board? Not sure how to go about moving it, but maybe someone in there would know what's going on here.