Universal Restore boot disk not working? Windows wants to run windows repair

I am attempting to port my system over to new hardware (new Motherboard and processor). I made a universal restore boot disk with the proper drivers for the motherboard, reconfigured my hardware, and started up, telling the computer to boot from my boot disk. I initially ran into an error 0xc00000e9 saying that there was an in-out error (this seems to have gone away after I turned off an external drive) and afterwards I am given the choice to go into windows repair, which doesn't seem to connect with Acronis software at all (or have any success starting the system). Should I say to start normally in hopes that the Acronis software will then kick in?