If that checkbox is checked the updater fails at the registry backup and changes step and a rollback is done.
Can you give me the full error? What systems is it failing on (Windows XP, x64/x86, etc.)? What's the exact registry change that fails?
Unchecked it works fine except that on 64bit systems the wrong registry tree is updated (as expected).
Why do you want to use the WoW64 emulated registry for a value that's used by the system? That is, Windows reads these values when the checkbox is unchecked (whether you're updating an x86 or x64 version of Windows).