Ignore the Open GOP warning. I get that all the time.
Reave, when I've analyzed these interlaced files in DGIndex, I've noticed that they're called "NTSC" and the non-interlaced ones are called "film". Perhaps it's simply a flag that, if ignored, will make the file usable. I've been re-encoding just because mixing the two types leaves those very issues you're talking about.
What directions in specific do you need? I do recommend simply playing with the program and learning all of its features. Also, check out www.videohelp.com and www.doom9.org ... they can answer far more in-depth questions on Gordian Knot.