There's only two times I've encountered any problems with the RTS.
1: Updating to the beta firmware, this caused old RTS files to be incompatible.
2: Loading a RTS on Brain Age 2 (Germ Buster minigame)
Specifically, loading the RTS after the title loads would cause a crash, but loading the RTS as soon as the rom boots is safe. (Yet, this causes Dr Kawashima's skin colour to change!)