If you start up homebrew launcher first thing when starting up your 3DS (im sysnand mode), then you won't see any of those installed .cias because sig check patches aren't enabled.
You have to start up a CFW, either in sysnand mode or emunand mode, /then/ access homebrew launcher, to access installed .cias on sysnand or emunand respectively.
That was one detail I missed. Nice catch.