Subspace and Allstars simply doesn't play well with any file replacement. 70% of stuff works, but if you are one of those people with a full 2 gigabytes of files, you have a lot of troubleshooting to do.
Don't change to USB, just don't. If they update your Wii, you can A. use a newer method to hack it. B. Use Smash Stack to launch gecko directly(You won't have to hack your Wii) Or if you're feeling dangerous C. Downgrade your Wii (Not recomended. Its the only way without being a retard to brick your Wii)
Uninstall gecko and try again, updates often directly attack HB these days. If that fails, use the Smash Stack method that loads gecko directly every time, its not optimal, but it works for me.
Riivolution is hard to use and still a little glitchy, if you really want your mods running now, use gecko, if you want to be able to run better stuff later, just switch back to Riivo, (and after using gecko, you will understand the concept much better)