That might be the issue then. The MMD is kinda picky about homebrew. However, I have a few things you can try:
1. Make sure your card is not corrupted. Worst case, you can copy all your data from your card, reformat, then copy it all back.
2. Make sure you're getting the very latest version from the official NES DS website.
http://www.cs.utah.edu/~tew/nesDS/
3. Try patching with both the MMD's DLDI file and the MMP's DLDI file. nesDS.nds can only hold one DLDI file, so you may wish to make a copy of it so you can have two separate files that are each patched differently. DLDIrc should have both of these files built-in, though you'll have to reinstall it if you didn't pick both the first time around.
That should at least get you to the file browser point.