All of those badges are "Destination" badges so only arrivals count. If the flight/activity occurred before the badges program existed, it will not count. Apparently if the flight/activity occurred before the badge was added to the program, it would not count either. If you do indeed have missing activity that should have counted, they will fix it if you contact them.
Take Three tracks by the segment. Every one way segment count as progress. Two segments equals a roundtrip even if the segments are completely unrelated.