Not sure if what you are talking about is the same issue I had, but it sounds similar.
I created several quick launch links in a few different groups. If I navigated to a different page using the promoted web links, the quick launch was properly populated. If I used any of the links I set up, then the quick launch would not display properly. Instead I would get a single group of links. No headers were displayed and no links from other groups were displayed. This even occurred if I navigated back to the home page from one of the quick launch links.
What solved my issue was adding a slash "/" (without quotes) to the end of the urls for the links.
site/SharedDocuments did not work (links disappeared)
site/SharedDocuments/ did work (all links displayed on the page)