Offhand make sure the hard drive is plugged into the outermost usb port on the Wii, else it won't be recognized.
Hmm I'm just looking over your older posts, looks like you had some trouble getting that Bootmii going. Could be part of the installation needs to be redone, maybe someone with more experience in 3.2-4.1 fw's will have more suggestions.
Aside from the usb port being in the correct position, you could try switching out the cable. I read in another post this solved someone's issue with the drive not booting properly.