FLY'N's performance is tied to its framerate, meaning that at 60FPS, it runs at 100% speed, at 54fps it runs at 90% speed, etc. Over the course of a 80min+ game, this adds up to minutes of lost time at anything less than a perfect framerate, and the game often dips below 60 in massive levels.

I first noticed this when comparing runs recorded in FRAPS to runs I'd done on Twitch recording only with OBS. I was consistently losing time on every split, even in autoscroller stages, and had no idea why. It turns out that while recording in FRAPS, with the "Lock Framerate while recording" box checked, FLY'N maintains 100% running speed even if the framerate itself drops below 60. You can even set lower framerates, like 15FPS, and the game will lock its speed to a consistent 25%.

FRAPS unfortunately isn't free, but it's the only thing I've found that can provide a consistent running speed for RTA comparisons of this game. I'd be interested to hear what kind of results other people get with and without using it, or if another method is found to lock the framerate. But if anyone pushes this game really hard in the future and consistently falls below my split times for no apparent reason, that's probably why.