Yes there is a work around for this but it only manifests itself when the MW server is 64 bit and the apps server is 32 bit or the opposite. If the operating systems are completely different then the merge steps have to be done manually.
What release of Maintenance Wizard are you on?
Since you are on the same machine the copy should succeed so you are hitting some sort of config issue I would guess.
Can you cut and paste the entire text box for the step?