It could perhaps be because you're re-entering levels that you've already been to. The Splits are designed, so that you only go through what you need to; it doesn't account for errors or different playstyles. There is also a different category, if you're not choosing to do water glitch.
If you don't wish to change your playstyle, you could also make the splits yourself, or undo splits that shouldn't have been making. As long as the livesplit ends when the credits start, you're good.
Perhaps try to add -gl to your launch options to force Hardware mode.
There is an autosplitter in LiveSplit. To activate it, go to "Edit Splits..." There should be a section called "Autosplitting and load removal by DrLa" Make sure you click the "Activate" button, then it should work.
I've also tried to figure out how to do this. Honestly, I hate it, but I guess it's a skill now: "Don't turn too fast"