Random guess but perhaps the spare drive isn't as good at reading backups as your old one (before it went pop anyway). The Wii drive isn't the best in the world and does give issues. Some people find that DVD-R from any manufacturer will work on their Wii, even DVD+R but others find that only quality brands like Verbatim DVD-R work flawlessly and even then only when burnt very slowly. I've heard that adjusting the drive can improve loading, but I've no idea how it's done or how good the results are.
You say you have to launch from the old backup launcher. Do you have no luck with Noegamma? What happens when you try?