I completed two keystones for the same dungeon, but Raider.IO only logged the higher key. Where is the other?

This is likely a limitation within the Blizzard leaderboards: They will save only the highest level M+ run by a given group of 5 players per dungeon. This means that if you run the higher dungeon first, then run the dungeon again with the exact same group of people, the lower dungeon will never register in the leaderboard. It is possible, for example, that Blizzard would save your +17 that went over time by 20 minutes, but not your 2-chested +16.

The leaderboard API is the only way we are able to detect runs being completed, so if it doesn't show up there we have no way to include it in your profile. We are hoping in the future that Blizzard expands their API to give us access to a group's entire list of runs, rather than just the highest level keystone.