Special Thanks to Mouks for figuring this out.

Watch the video to understand how to avoid losing your runs to the Blackout Glitch on N64.

The main thing is you don't want to jump out of the control room and back into it again. If you're jumping onto the Elevators or grabing the Token with Text Storage just make sure you commit to the jump and don't go back into the room.

Edit: This can also happen if you walk near the ledge, or use the grappling hook to go back into the room, be careful! It affects both Hamm's Room and the Race Area!

Edit 2: If you're on the control room and you think you accidentally triggered the "Blackout Glitch" you can quickly jump into the vent and out of it to reset it like shown below.