If you have cIOSCorp installed that would explain why your HBC is upside down.
If you want to continue using cIOSCorp and have your HBC the right way up use DOP-IOS to download a "clean" IOS 61. Then use the Hackmii installer to get to the HBC install and uninstall option. Once you have a clean IOS 61 on your system uninstall HBC and immediately reinstall it whilst you are still in the Hackmii installer. This should result in HBC being installed using IOS 61 and not IOS 36.
As as been stated above if you are not using CIOSCorp just use DOP-IOS to install a clean IOS 36.