I have just had the same upside down issue, heres how I got it and heres how I fixed it (sorry if there is too much detail) :-
I was following this guide on softmodding a freinds Wii
http://gbatemp.net/index.php?showtopic=168890 as I softmodded mine ages ago with the twilight hack and had never done the banner bomb method
I had followed the guide flawlessly (I work in IT and I am used to doing things like this on equipment that costs more than my house)
I had completed sections ,
Getting HomeBrew and BootMii,
Backing up your NAND and was on section
Patching IOS36
I had used downgraded IOS 15 to patch IOS 36 Then I got the upside down homebrew
I searched and found this thread,read about the same problem and rather than reinstall homebrew channell I used my SD card out of my wii(I was doing this on a freinds Wii) with my homebrew channell files on (completely seperate files) same problem. After reading previos posts I figured the issues was with IOS36. As my SD card still has all the files I had used to softmod my wii before I found the awesome guide above. I used Waninoko's wad manager 1.4 and installed IOS36 (IOS 15 was still downgraded from the above steps) off my SD card (IOS36-64-v3094.wad) and the homebrew issue was fixed. I then used Trucha bug restorer to restore IOS 15.
I hope this helps anybody else with the same issues or anybody trying to fix this. I don't use forum's that much so apologies if I have posted in the wrong place offended , included too much or not enough info.