Using an R4i Gold (r4ids.cn)... When I try to enter the Nintendo WFC on Pokemon Black, the connection the 3DS is connected to no longer gets connection... And yes I'm using WEP encryption, even tried no security.
Does it give you an error code? Are you perhaps accidentally turning the Wifi switch off by chance? I feel like I've seen this problem before and it was fixed by a system format but I'm not 100% sure...
When I enter Union Room on Pokemon White, the network coverage becomes red instead of green (filled with bars)....... I just tried a different game like Mario Kart DS and it actually ran normally.... I dunno what's wrong with Pokemon
I've setup my Nintendo DS connections too under internet settings, and it still makes certain games react badly to the WFC or Ad-hoc features, especially games like Pokémon Black/White and things like the Entralink. That's the most notable exception I can find at present.
EDIT: It's worth noting that the stupid wireless switch has to remain on at all times for that to work, but even so, I have had no end of issues with the AdHoc features, such as the Entralink, etc...but I think it's really dumb it has to be on all the time for a DS Game to work as intended. Because the original DS never needed it on 100% of the time.
This has caused me no end of headaches as well. I ended up connecting a cheapo cable router to my isps router. It has no security. I switch it on only when I wanna play online with a ds game. Its sadly the easiest way.
Had issues with DS wifi on 3DS myself. Regardless of flashcard usage. Worked fine with 3DS-specific wifi, just not on the DS side of things. I'd get an error code every time it would do the connection test. Would recognize the router but would fail when testing it. I ended up contacting Nintendo and they told me i had to reformat the system memory. That did actually fix everything. Though your 3DS will lose all its apps and settings, acting like it would as you first bought it (though it retains the latest firmware update). For me however, the eshop did recognize all the games and apps i had already downloaded, including ambassador ones. It let me redownload them all for free. I lost all the Mii related things though, as well as my 3D puzzle swap stuff. No big loss though in order to get DS wifi working.