I don't know why the problem you're describing would happen if your card is properly formatted. I do not use my microSD's root for any files except an icon file and autorun.inf file so that the card shows up as my "Supercard DSTwo" drive when in my PC.
All of my roms, homebrew, and videos are in sub-directories. However my set up does include a bunch of plugins.
I am also using the iMenu homebrew interface instead of the official interface. I will link the guide I used to set-up my card.
http://gbatemp.net/t260979-imenu-step-by-s...set-up-tutorial
* Followed steps 1-8, but I also had to download the updated version of the iPlayer plugin from the official site to get that feature to work instead of white screens on load.
* I made additional directories for different types of ROMs and for video files. (I used www.keepvid.com to direct-download some Youtube videos - higher resolution FLV movies will not play well though! Lower-res plays best.)
* I then set all of the directories that I didn't want to see when browsing, as Hidden files, including all their subfolders and contained files. This way I see only rom/homebrew/video directories while browsing when using the various emulators and the DS Game feature.
* I also updated the cheat database using the usrcheat.dat file from http://cheats.gbatemp.net which belongs in the "_dstwo" directory.
-- If you want me to find you the guide about updating the DSTwo firmware to work with DSi-FW 1.4.1 (so you can use the DSiWare Shop) I can look for that too.
All of my roms, homebrew, and videos are in sub-directories. However my set up does include a bunch of plugins.
I am also using the iMenu homebrew interface instead of the official interface. I will link the guide I used to set-up my card.
http://gbatemp.net/t260979-imenu-step-by-s...set-up-tutorial
* Followed steps 1-8, but I also had to download the updated version of the iPlayer plugin from the official site to get that feature to work instead of white screens on load.
* I made additional directories for different types of ROMs and for video files. (I used www.keepvid.com to direct-download some Youtube videos - higher resolution FLV movies will not play well though! Lower-res plays best.)
* I then set all of the directories that I didn't want to see when browsing, as Hidden files, including all their subfolders and contained files. This way I see only rom/homebrew/video directories while browsing when using the various emulators and the DS Game feature.
* I also updated the cheat database using the usrcheat.dat file from http://cheats.gbatemp.net which belongs in the "_dstwo" directory.
-- If you want me to find you the guide about updating the DSTwo firmware to work with DSi-FW 1.4.1 (so you can use the DSiWare Shop) I can look for that too.