I delved deeper into framerate issues only to find out that each source VOB file has it's own framerate. Now I regret choosing such a simple editor as KDENLIVE as I cannot make the different framerates work together.
I did however get an idea - I'll render separate parts of the whole project, each with it's own corresponding framerate and then join them in AVIDEMUX. I have tested it on two smaller samples and it seems to work.
I was almost out of ideas.