If you use a Retroarch emulator, with any core, your run will not be accepted.

As exposed by @garadas21, Retroarch lag reduction is deliberately making the emulation less accurate, in order to make it play faster.

There are a number of other emulators that are accurate. Please use those instead. Examples: Nestopia, Fceux, Mesen, Higan, or OpenEmu with one of the above cores.