With Veictas' autosplitter it was possible to track the time loss in individual levels and spot a weird glitch: it seems like the game deteriorates as the game's session ages, resulting in a consistent and ridiculously big time loss after several playthroughs. In my case, we are talking about 0.5 seconds of unavoidable time loss on stage 1, which is a lot and which magically disappears if I close and open the game again. The available solution right now is to start a fresh game session as soon as you notice important time losses. Ideally you'd want to start a new session on each attempt, but the game is already enough frustrating on its own. It's important to notice that this is just what I have experienced and I'm not sure the game works exactly the same on different setups. If anybody has more information or workarounds feel free to post them.