Now this so far seems to be an issue that only affects me, but in case it affects others I'm putting the solution out there. With some games, not all, after enabling cheats the game will fail to work, but will work with cheats disabled. If you have this problem, the solution is to hold down X while booting the game, and it should work fine. This doesn't affect everyone though. Hopefully this information becomes useful to others.
I was about to make a topic about this. Glad I found this post. Expanding upon this, you need hold X early and you will know you did because "Loading" will change from blue to red instead of green. What's interesting is that Kingdom Hearts 358/2 Days always has Loading change to red, with or without cheats. I wonder what it is that is different about that one.
In case anyone was wondering, I have a DSi and I'm using an Acekard 2i. Not sure if either of those details are related to this minor inconvenience which will be hopefully resolved with the next release.
To (almost) all of the recent complaints about freezing, you sure it isn't this? This was the problem for me. However, this does not solve my problem with soft resetting a game I have codes enabled with. Seeing how you had to hold X for it to load, I am guessing one would have to hold X as you press L+R+Start+Select to soft reset. I tried to do this and I either did not succeed or this just isn't how it works. I'm pretty sure it is enabled cheats since the game soft resets just fine if I leave cheats disabled.
As a side note, Kingdom Hearts 358/2 Days has that "Title Screen" option in the menu rather than soft reset capability. However, whenever I select it (Yes), the screen goes black and stays as such.
Any methods known to deal with these issues?