I'm not sure what kind of error this is, but I can give you a few random ways that always does their job well.
If you are running games in Clean Mode, please skip to Solution #3
1) Check to see that you've downloaded the correct version of the DSONEi EOS, not DSONE EOS's.
2) Backup your files on your Micro SD card and Format it. After you've finished formatting your card, copy fresh EOS files to the card.
3) I think I may know the reason why you can't open the In-Game Menu anymore. You're saying that opening the In-Game Menu used to work for you, correct? If so, then I think you ran some games in Clean Mode. If you ran games in Clean Mode, you can't open the In-Game Menu during a game nor can you use cheats, hence the word clean. So check to see whether you ran games in Clean Mode. That may be your problem. If you are running games in Clean Mode, then just switch to running the games in Patched Mode.