I created a new project and copied the content over, hoping to avoid some of the clutter and issues from previous users and start fresh with my own css and all of it.
However, in the new project - with same stylesheet and page layout - the pdf TOC uses madcap's green, very light text from madcap, and not my toc styles
update: found this by opening the stylesheet in a text editor, but still not clear why it wasn't using my styles. Also noticed some changes I made in the stylesheet editor in Flare were NOT appearing in the stylesheet, so added them manually.