Due to the way Flatpak deals with nvidia drivers, you need to run flatpak update after any time the nvidia drivers update and you reboot the system. Thankfully you do not need to reboot after updating only flatpaks. Could not find a good source for this now, unfortunately.
As for the "why?" - flatpak apps do not contain the userspace parts of the nvidia driver required to use the GPU properly, they come packaged as separate runtimes. These nvidia driver runtimes need to match the specific driver version you are currently running. If they don't match, flatpak downloads the right runtimes when updating.