@ mimi and wiixale,
If your HBC uses a patched IOS61, it will be upsidedown. If it uses a patched IOS36, 90% of the time u launch an app it will blackscreen.
easiest way to fix it is to use yet another wad manager mod to install the wads (IOS61 and IOS34). You can also use dop-mii (I personally would only use dop-mii if I didn't have the wad and wanted to download it from NUS on the fly... dop-mii is also great for patching IOSs on the fly, but we do NOT want to apply ANY patches (including ES_Identify and NAND permission patches). Use any method to launch yawmm or dop-mii (HBC, bannerbomb, wiixplorer, etc.).
After you finish this, launch the hackmii installer (either via bannerbomb, the HBC, wiixplorer, etc.). Then reinstall the HBC (no need to uninstall it first). If you haven't installed/updated bootmii and dvdx, you can also install those at this time. Exit the installer, it should return u to the HBC, and it should be running smoothly on a non-fakesigned IOS61 now (hit home to confirm). (note that if your HBC was already installed to use IOS61, you don't need to reinstall the HBC... but it doesn't hurt)
I apologize to the configurable USB loader team, this has gotten way off-topic... @ mimi and wiixale, if you have more questions on this, please post them in an appropriate thread. I don't mind if u ask in my NUS Auto Downloader thread since it is somewhat related (since it has this solution as an option), but there are probably many threads that were made specifically for this issue, and I'm sure any questions you might have, have probably been answered already in those threads.