1/ some .elf files migth not boot anymore with newer HBC because they have a wrong format, use boot.dol instead for Wad Manager (but don't simply change the extension, it obviously won't work, look for .dol versions, they exist)
2/if you updated to 4.2 using Nintendo official update, they are installing IOS249 as a stub (which means it does absolutely nothing when loaded) and this will overwrite any custom IOS you had in that slot. When Wad Manager starts, it load IOS249 which crashes since it's now dead code.
Look for solutions on how to re-install a valid cIOS under 4.2, not sure if it's possible though since theofficial update mostly replaced ALL your vulnerable IOS during the process.... I f you had a cIOS installed as IOS250, there *might* be some hope...