That's like the issue that I used to have. Now I have to wait a few minutes (so much time for me) to play a game. The only way that I get to fix this was installing unlaunch. Unfortunately I just have a DSi, I want a 3DS but I can't. I used to launch twilight menu++ from a dsiware exploit (Sudokuhax Installed with flipnote studio) and always appear this white screen after the NDS-Bootstrap "please wait" (3 minutes to just see a white screen). I don't know why this happens, but just with unlaunch I "fix" it ( and I said "fix" because I miss the 3DS boot animation).
How many ways do you have to launch twilight menu++ on a 3DS?