How incredibly odd... 

I have limited technical knowledge of the game (Simion32 is far better qualified in this department), but as a guess; perhaps a layer visibility or level lighting flag (like in Blackout Basement/Loopy Lights) was triggered by something you did while optimising your run. 

Is this a TAS, or a regular speedrun? 
What console/emulator are you using? 
Welcome to DKC Atlas, by the way; hopefully someone here can help solve the mystery. 
