It may happen especially for small third party airfield addons, that those airports/runways has not been caught by "makerunways.exe" so runways.csv will not include some runways. In this case you will have to manually add to the created runways.csv Airport/airfield ICAO code, coordinates, runways, runways length, alt of rwy threshold etc. Then rebuilding PF3 database should catch missing airport/airfield/runways if added correctly.
Tweaking and digging in files of addons is the price what we must pay for the simulator made not perfect by main game developpers, heh:)