Yeah, it seems to be a common problem, though some people have managed to get it working without any issues.
I was hoping 1.3b would solve the issue but the release only provides a .3dsx version, so I suppose we'll never know unless we compile it ourselves.
I have the same issue, and today discovered a workaround: launch BlargSNES with FBI (look for title CTR-P-BLRG) and it works! Still just hangs on a black screen if I try and launch it from the home menu though.
(I'm on O3DS 9.2 rxtools linked emunand)
(oh and 1.3b is just a hotfix for the 2.5 *hax, so doesn't need a .cia version)