It’s pretty much as I said there. Unfortunately I can’t tell you the exact error because I wouldn’t know how to explain it anyway. 
What it seems was happening that only a player’s first score on each route was being reported and any other attempts - even if faster - were not being picked up properly. However in the first few days there was still some movement on the leaderboards due to people posting very fast times on their first tries which gave the false impression that things were updating.
Once players started pointing out the times were getting a bit sus we gathered the reports and were able to identify the flaw. @Elsebeth_Rhiannon helped me with some troubleshooting too, so cheers!