imported files not lineing up, used awextract?

i am using aw.exe in order to control my mixing recording with an aw4416. But, after running awextract , i then try to import the files and when they do go into cubase, tracks are not lined up, time is way off between tracks? How do how align my tracks so they will be in the correct time with each other? I am using Cubase Elements 6, on Apple 10.7 OS.