Hmmmm, ideally we need to know if retail DS carts work. Unfortunately I think you will run in to the same problem with out of region stuff.
Ok so lets try this, use 3DNUS to download and install the following title and install it to both emunand AND sysnand, then see if the carts work again.
0004800F484E4841 v0
This is the initial version of the DS Cart Whitelist. You will need to install it to both sysnand and emunand in order for things to work properly (not 100% sure its needed sysnand but it won't hurt and better to be thorough). If your emunand is on 9.7 or higher you will start to get update nags because the title is out of date, but for right now we are just testing to see if it fixes the problem so ignore them.
After installing it, test your ds flashcart to see if it works. Keep in mind that there are some flashcarts that will not work at all on a N3DS because they were blocked with updates to TWL_FIRM and we cannot easily mess with that on the N3DS.