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It's a player problem.
If you created a full disc backup you should have seen a log line "will verify M2TS hashes". If you got no hashcheck errors, then your files are guaranteed not to be corrupt.

But, if it's a player problem, why do I see the same problem in the same locations using multiple ...

Well, I found that Harry Potter and the Deathly Hallows Part 2 has the same symptoms... when I do a full disk back-up with MakeMKV, it corrupts the copy. There are numerous places throughout the movie where it stutters and pixelates like a corrupted h.264 file.

As an additional experiment, I used ...

I own the 11-Disc Region-Free Box set - "Harry Potter the Complete 8 Film Collection".
I used MakeMKV (v1.7.9 for winx64, installed under Windows 8 Pro, 64-bit) to make backups of all the disks. I chose the full backup option, just removing the encryption (not making MKVs).

The first 6 movies all ...