I had similar failures with either waypoints … or no waypoints. At least I could not detect a big difference there. It feels “stochastic”.
But “crashing the aircraft” after arrival so far consistently registered all flight minutes and all takeoffs and landings during the flights.
It feels to me like all the internal “logging” is OK … but the final “commit” into the Logbook only happens unter certain conditions. The most reliable condition (so far 100% for me) seems to be … crash the aircraft on the final destination (e.g. into the terminal or whatever)