I've had this problem before with two specific wads:
StarFox 64
Cruis'n USA
What's probably happening is that you either have bad Wads, or they're interfering because you had them installed before.
If you're sure they're not bad wads, try the following:
When you try to install these wads, select them, and instead of choosing "Install", choose "Uninstall" or "Delete".
It won't delete your Wad file, but it will delete stuff left over on your console. After it's done deleting/uninstalling, try to install them, and they should be installed now.