I'm having the same issue. It was first working fine but then I tried loading up a new source menu, and it gave me the DSI error. When I went back into the source_menu.ini and edited it back to no it took the DSI error screen away but it just boots into a black screen now it's really annoying because sometimes I forget to take out the SD card when turning on my Wii . So now I have to take it out then pop it back in after it loads to get this to stop. Glad to know someone else is having the issue now it's time to figure out how to fix it.
Under this thread the bottom has a link to show sorta how to fix the issue. I have an SD card not a usb harddrive with the issue but I don't know I need to read it over I suppose just to make sure theres something I can figure out . check it out though maybe it'll help you.HTML:http://gbatemp.net/threads/emulate-a-wii-nand-to-keep-your-wii-clean.291814/
I was finally able to fix the issue. I'm not sure what caused it to work exactly, but I reinstalled Bootmii to Boot2 for the 100th time and it seems like it might have been more successful that time around or something. I also realized that I never installed the Wiiflow Channel to the actual NAND so that was the other thing I did (I'm not entirely convinced that was the fix, but you never know). Either way, it works now and I'm not complaining.
sirxup,
It sounds like your issue might be slightly different than mine. How are you booting into WiiFlow (Priiloader, Bootmii Boot2)? Also, it doesn't hurt to try renaming your Wiiflow.ini and your WiiFlow folder on your SD root and let it recreate everything. I'm not sure where all of your WiiFlow stuff loads from, but the WiiFlow folder and dol all load from the SD for me. The EmuNAND however is on the USB. Also, make sure your sneek stuff is setup correctly. If you're unsure, it might not hurt to grab a copy of the Sneek folders from Abz pack. I know some of this stuff doesn't sound like it could cause issues with booting WiiFlow, but if there's one thing I've learned from troubleshooting this stuff, it's that you just never know.