I'm not sure of that exact issue, and have never personally heard of it or encountered it, but to try and identify where your problem lies, you should first (If not already) install a recent version of Neogamma. Next, try and run your Gamecube Backup through Neogamma. If the GC Backup does not work through Neogamma, it would indicate the problem probably lies with the Mios install (Presuming the game is said to work on the compatibility list), in which case, use Any Title Deleter to remove the Mios, then re-install it (make sure you are using the installer from GC Backup Launcher 0.2, if not already). If the Gamecube Backup does work through Neogamma, it would indicate that your problem lies with GC Backup Launcher itself (or the forwarder if you are using one). If you arent using a forwarder, delete your GC Backup Launcher from the Apps dir on your SD Card, and download a new copy of version 0.2, then put it back on your SD card, now try it again. If you do use a forwarder, then first try to run GC Backup Launcher directly from the HBC, if it doesnt work still, delete it and get a new copy (like mentioned above). If it does work, when running directly from HBC, it would indicate your forwarder is bad, or it is pointing to a different path than you have installed GC Backup Launcher to (the usual path, for forwarders, is SD:\\Apps\GC_Backup_Launcher\Boot.dol).
I hope that helps you to, at least, identify the problem, and hopefully to then rectify it. Good Luck with it.