Video Quality Estimator has a possibility to auto synchronize files in case they do not start from the same frame. Click the checkbox “Use auto synchronization window (frame count)” when creating a new task, then set up a range and select which streams should be synchronized (A-B, A-Raw, B-Raw).
Video Quality Estimator searches for equal frames among this range and offsets one stream toward another. The more frames in the stream, the more range is required.
Synchronization could be done manually. To do that, clear the checkbox “Start quality estimation after closing this dialog” when creating a new task and click OK. Then select the necessary file (A or B or Raw) in a pop-up window and increase / decrease its offset using corresponding buttons. When you have done synchronization, click Play to have objective video metrics calculated.