Skip all the boring stuff take me directly to how to fix it.
How to fix it
Install Original IOS34-v3348
using WAD Manager 1.5
and reinstall HBC using the Hackmii Installer
if you can not run wad manager, launch Pimp My Wii using bannerbomb.
Team Twiizers has been kind enough to create and update the Homebrew Channel. Thanks you guys rock.
Team Twiizers has also been kind enough to cause the HBC to invert if the IOS used to run HBC has been modified. No thanks.
This explanation is given using all updated, unstubbed and currently available original Nintendo IOS.
By Default, Homebrew Channel 1.0.6 will run using IOS61. If this IOS is modified then the HBC will become inverted. Depending on your IOS patches during the installation of HBC it could be running from a few different IOS versions.
The popular method to fix the inverted HBC is by installing original IOS36. However this is a bad idea. There are many apps which require the use of a fully patched IOS36. [and not to mention cIOSCORP :argh: ].
So if you then reinstall original IOS36 your apps which depend on IOS36 being patched will no longer function, including games launched from disc channel which run using IOS36 by way of using cIOSCORP and even a modchip.
The best method is to install original IOS34-v3348. This will allow HBC to run from IOS34 and allow for every other IOS to have patches.