Strange, that’s never happened to me, projects always have loaded fine when changing computers, or after rebuilding/repairing from a catastrophic failure of the same system, but I always got a pop-up asking me to point to the location of my project for each is all.
Could it be that the old projects had VSTi’s that the new computer doesn’t or can’t run certain old VSTi’s or plugs? I don’t see how midi can affect it this way. Did you go from a 32 bit to a 64 bit OS?