I'm also having some issues with the R4i Gold RTS. I created a first forwarder (Picross 3D) to test the waters and see if it was working as intended, although it didn't have the DS startup screen. Turns out it worked just fine.
Then I created some more forwarders. I tried them all yesterday and everything was working perfectly, with the DS startup screen. But today, I tried to load Dragon Quest IV and it sent me to the flashcarts menu. I updated the files with the new version on the first page of this topic... and every forwarder started booting Picross 3D. I deleted the Picross 3D forwarder and... the forwarders still booted it instead of the game they were supposed to boot.
I tried using an Acekard 2i, but now the Forwarder3DS program refuses to open most of my games, and some of those that are opened by it either display a blank icon or have completely messed up titles. Yesterday everything was working as intended! I'm about to give up on this and just use my flashcart as always, until DS ROM booting from the 3DS microSD card is implemented
Edit: Tried on a different PC. I get the same results with Forwarder3DS. I don't know why it's not working now when it was yesterday. I'm just giving up on this...