Update: I have updated my 3DS to V5.0.0-11, have tested all the cards i have, currently only r4i gold 3ds DStwo, r4idsn 3ds and ace3ds plus flashcart can work on the latest 3DS firmware.
Update News: It has been confirmed that the 3DS has been updated to V5.0,0-10
Changelog of the 3DS V5.0.0-11
UPDATE - Details on the firmware from Japan's official site...
Major changes by updating to 5.0.0-11
● improve the convenience of "Nintendo e shop" (※ 1)
In sleep mode during startup "Nintendo e-shop", we are now able to receive later unawares communication.
In addition, and will be able to receive at a later "update data", we have improved the usability.
● Responding to save data takeover tool
For details, "To move the saved data to the download version" refer to.
● Improved system stability and convenience
So you can enjoy a more comfortable, we improve the system stability and convenience.
● eShop font now matches that of Wii U
● loading bar has changed in the Internet Browser
Notice
Currently do not update your 3DS or 3DS XL to this new firmware if you want to use flashcart. Because we don't know whether this new 3ds firmware blocked the flashcart yet. Will test my 3DS and cards soon then send the update here.
Do not update your 3DS unless you have updated your flashcart!