There isn't a configuration setting for that. If you want a certain splashscreen to run only once, then you'll have to run a script on first boot that will switch the video files - same name, different files.
@Aaronero It's not the emulator that's showing the splash images, it's the Runcommand, so there's nothing that the N64 core (or emulator) is doing. Runcommand is using fbi to display the image on the RPI, but it's not doing any scaling by itself, it just tells fbi to try and zoom the image as best it can.
You didn't say anything about your system - as requested by https://retropie.org.uk/forum/topic/3/read-this-first - so you may not even be using the latest RetroPie or there's some other configuration that might interefere with the image splash.