I'll admit I'm not too familiar with the built-in Auto-Splitter in LiveSplit since it wasn't working well for me. Either way, the reason why there's a 1.36 delay is that AutoSplit64 detects when the logo pops up, but the game actually restarted 1.36 seconds before that first recognizable frame.

If you're using AutoSplit64 to have your splits done automatically, starting timer is at 1.36.