Think i may have found a solution -my hdd was working with all games apart from new mario bros (i use wiiflow to load games), but then had this same problem after updating to 4.1e with the intent of getting mario working. Installed all hacks, custom iso's etc... only to find that opening wiiflow bought up all the games, covers, etc.. ok (indicating a working drive) but when i tried to run it i received a black, hanging screen.
My solution was this - for some reason when my cracks have been installed something seems to happend to the display settings. If you try to open a game in ntsc when running a pal system the result is usually a hanging black screen. Now even though my system settings are pal i have to set my video to pal, or auto patch. If i leave the loader to get its own default settings it doesnt work.
Dont know if this is the same for everyone, but having certain games working would imply that they are possibly different video region settings. Try messing about wih your video / region settings in your loader & see if it helps.
If it works let me know - ive leached good advice of all these forums for years (mostly because ive never had anything constructive, or interesting to say) so it would be nice to finally give abit of help back
Dan