Topics Being Duplicated Within TOC

I'm running the new TCS 2.0 - authoring in FM and importing into RH. My problem is this: everytime I do an Update All or Force Update All (still haven't figured out what's the difference between those 2 yet), the TOC in my project gets all the same topic headings created again, but just added onto the end of the existing topics. I end up having to manually delete the duplicates to clean up the TOC before I generate the .CHM.

Is there a setting somewhere that replaces the TOC with the updated topics from FM instead of adding on?