Comparison on MTP device stopping for no apparent reason

[DaWrecka]

Up until a couple of nights ago I was able to synchronise files between my PC and two different Android devices without problems, but today the comparison keeps stopping at some point - "Items found" will stop incrementing and the "Scanning" prompt will stop updating too, but the timer will continue to go up - until I click "Cancel" at which point the entire application will stop responding. Obviously, if the comparison fails to complete, synchronisation is impossible.

One of the devices is a Polaroid P791 running Android 4.4, and files are being saved on the microSD which is formatted as FAT32; the other is an STK Sync 5e running Android 6.0.1, and the SD card is formatted as encrypted internal storage.

In each case, it's a file that was transferred to the device days or even weeks ago. I updated to FreeFileSync 10.1 but that didn't change the situation. I rebooted the PC and it didn't help. I rebooted both devices, and that didn't help either. However, what did change the situation was when I removed the SD card from the Polaroid and connected it via a USB reader; after I updated the destination paths, comparison completed with no problem - unfortunately, sync failed again when the process stalled hard on one file, but the application didn't hang completely at least. And connecting the SD card to the PC directly isn't an option at all with the phone, since the filesystem is encrypted, so I still need a fix.

I don't know if there's any logs I can check to find out what's happening, and all I can find in Event Viewer is the notifications about the application not responding and being killed.