The time that it shows in the result screen is the accurate one. Not sure what causes the glitch or how to prevent it, but runs will be accepted based on the time in the result screen.
As of July 7th, 2018, fadeouts before and after loads will now be included in loadless timing. The load remover tool has been updated to reflect this change, and it is required that you update it for future submissions. Any submissions after this change that do not use the updated load remover tool will be rejected. All current runs on the board are being updated to reflect the new timing rule.
The reason this change was made was that upon the multi-platform release of NST, we found that the PC version of the game saves approximately 2 seconds per level over other versions of the game just on fadeouts alone. This was deemed as an unfair advantage, and we found this to be the best solution possible.
TO ALL RUNNERS: Feel free to re-time your runs with the new load remover tool and resubmit them! We have a giant workload ahead of us in re-timing runs, so any help is greatly appreciated!