I would guess you just have a mixed source on your hands.
Read the Bible on the basics of dealing with interlaced content and how you can check with your eyes what it contains: linky
So, basically, if things really are as you say (since you don't know about the basics I'd guess you want to go around your DVDs once more and see if they really contain what you think they contain) : 1) you have 24/1.001fps sections everywhere else and 2) 60/1.001 fields per sec credits overlaid on X type of stuff on the credits scene.
How to deal: tfm/tdecimate other parts and deinterlace the credits (bob to 60/1.001fps from which you selecteven to 30/1.001fps)
Then just see the output on which framenumbers diff. parts start in the end result and make a short v1 timecodes file. Example:
#timecodes format v1
But really, just read TheFluff's text on interlacing, pretty please. And see in AvsP/VirtualDub what the stream itself looks like. You will understand much more after you actually understand what you're dealing with
And yes, reading the documentation on everything you use does actually help as RiCON said.