you didnt even give us any background of what your setup is. we have to know things like that to help you know.
oh sorry about that. Im using r4 and I downloaded the latest firmware(v.1.1) and there was a feature that said that i can turn on/off codes in the middle of the game and the site didnt even say what buttons to press. is that information enough??
I did a quick google of "r4 real time cheat" and actually came up with this page first ¬_¬ not a good start... Anyhows I found it and the combo is L+R+DOWN turns the cheats off (they're on by default) and L+R+UP turns them back on. I digged out my old M3DSS (was buried under all the rubbish on my desk) spent ages looking for my microsd (turns out it was in my EZFlash) and stuck it in my DS and tested it with New Super Mario, i used the freeze timer and the always 99 coins cheats. When I disabled the cheats the 99 coins cheat stopped straight away, but the timer stayed frozen untill i reloaded the level.