Yes, you've been playing correctly. You resolve all secondary results of the initial fire before rolling for the next.
From the Turn Order cards (not sure if these were included in the initial print run):
2. Advance Fire
- Roll for Smoke
- Resolve Explosions (if needed)
- Resolve Flashovers (if needed)
- Resolve Hazmats (if needed)
- Resolve Flare Ups (if needed)
- Resolve Knock Downs
- Resolve Lost POI or Victims
Edited to Add: So, actually, I guess not all secondary effects, but I can't think of a situation where it would matter if you removed a Firefighter or Victim/POI before rolling for the Flare Up.