Connection via MSC gives more than MTP?

Hi

I recently started testing some file comparison applications and I kind of wish I hadn't.
In running comparisons between files transferred from my Sony Z2 (Android 5.0.2) and Windows 8.1, I have found that sometimes, files are not fully sent over MTP.
I have transferred 106 video files from my Z2 over to my PC. Five of the files have been highlighted in a file comparison programme as being different when transferred over MTP.
I have finally found that the problem is MTP.
I have attached 2 copies of the same file - shot on my Sony Xperia Z2.
At first glance it's just a quick video I took on an evening Thames cruise in London. The end of the video is important, MSC shows a man's head moving towards the bottom right hand side of the video at the end, the MTP version doesn't get that far.

MTP
https://www.dropbox.com/s/iznshi5dat...99MTP.mp4?dl=0

MSC
https://www.dropbox.com/s/u7dh42bt32...99MSC.mp4?dl=0

What's causing the problem? I'm really happy to test any suggestions and report back.

Thanks