One possibility that I just thought of: When I downloaded the host backup, MS Security Essentials found a couple of backdoors that it quarantined and also 2 tools that it quarantined. Is it possible the tool signatures are for tools being used by the migrate.software? The two tool signatures that were quarantined were "Tool:Linux/Psybnc.A" and "Hack Tool:Linux/Xhide.h". Could one or both of them be needed for the migrate? Could the migrate software be calling for a module that is being quarantined?
Do you want a copy of the host database before it's used for the migrate or after it's been modified on the local computer by the migrate? How can I get a copy of it to you?