Hi There,
I was having the exact same issue and came across this Technet article: http://technet.microsoft.com/en-us/library/cc431366.aspx
Basically you have to reboot back into WinPE (if using USB/CD Media) so that it can properly map the drives and lay down the OS Image (simplified explanation).
I ended up putting another Restart Computer step right after the Format and Partition disk steps in my MDT Task Sequence.
Hope this helps,
Dustin