Problems encoding a show that was detected as a hybrid

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I encoded an episode of a show I recorded with SageTV and my Hauppauge 500MCE tuner card and I noticed some skippy scenes during playback. I used ShowAnalyzer and VideoReDo to cut commercials and that made the show ~22min long then I used AutoGK to encode it with a minimum width of 448 and set the size to 1/4 cd. The show has a lot of camera panning motion, and mainly in those scenes when the camera pans it becomes very jerky/skippy for a few seconds. I checked the log for the file and it said Source is considered to be hybrid (mostly NTSC). What does hybrid mean and what does AutoGK do with a file that was detected as hybrid? I noticed that there was 2 options for dealing with hybrid files in the ctrl+F9 options: Force IVTC and force Deinterlacing, whats the difference between them? Which one should I use? Thanks in advance for any help.

If you have any tips on how to improve the quality of encodings, feel free to share ;)