If you've got a problematic (or) NTSC source, you have to perform IVTC (which means InVerse TeleCine).
IVTC allows you to encode the source at 23.976fps instead of 29.97fps which results in better quality at the same size, but it takes some extra steps.

Since I don't have any DVDs that are problematic, I can't say anything about these steps from personal experience. I don't want to provide false and/or incomplete information, therefore I suggest you check out the IVTC guide by doom9.org.

You need TMPGEnc and the TMPGEnc VFP plugin for this guide; follow the steps provided there.

Then continue with step 6 (VFAPI conversion) of my guide and open the TMPGEnc project file instead of the DVD2AVI one; you still need the audio track from DVD2AVI though!

Sorry for any inconveniences.