I've had an R4DS for a few months now, and it was working great, but newer games claim they cannot load/read the card. I know that the games are on the card correctly, since each error message is unique to the non-working games. The two in particular are Contra 4 and Ninja Gaiden DS. Is there like new software I need for newer games? Or has Nintendo finally wised up and offered some protection against flash cards?

Make sure you've updated to the latest firmware for your R4 (which I believe is 1.17). If that doesn't work, you may need to reformat your memory card or download your ROMs from somewhere else (don't ask for ROM sites here, though).