I used to do everything in AviSynth. I would mix my Videos and call Batch Files to compress with x.264/5.
AviSynth also has Math Functions like Compare which compares Frames: http://avisynth.nl/index.php/Compare - Not difficult to write a Script that grabs a few Frames whenever there's much of a difference and create a Visual Report (a Video of the excess differences).
A Program that did everything perfectly is likely to be expensive due to a limited Market (with rich customers) and a Test that simply gives you one number doesn't necessarily mean much nor does it identify the problem - if it's a single dropped Frame would you want to spend hours recoding (possibly with the same result).
If you want to Automate for a low cost you'll have to learn to write the Program or simply do it with Scripting - AviSynth is designed for this sort of problem.
There's a reasonable chance of finding the Script written for you but the URL above gives a couple of examples of how easy the Language is to learn.