We can dig into the logs if needed, and isolate the scans to one folder set at a time to narrow them down.
The first step, though, is absolutely to check the disks themselves. Even if they're new. In fact, especially if they're relatively new. New disks are always a risk until they're good and broken in (infant mortality is absolutely real, even if
the observed bathtub curve isn't as deep as modeling would predict). If they're external disks, the power supplies are much more likely culprits than the disks themselves, by the way. The power supplies included in most USB enclosures are the absolute bottom-of-the barrel variety, and are the most common way those disks fail.
But more likely than a hardware failure is filesystem problems. This can be caused by a variety of factors, but sudden power or data-connection loss is the most common. Unfortunately, with external disks, this happens all too frequently (a cord gets yanked without properly dismounting the drive, and if a write was pending, you're left with filesystem damage). But, chkdsk will almost certainly fix that up if that's the case (or, at least, detect it).
1. Run chkdsk on all drives that MC watches, and on the system drive too.
2. If the manufacturer of your disk provides a decent hardware health utility, run at least the basic tests on each disk. You can't usually do the write tests (which require a blank disk), but you can do the basic and deep check tests. If the disks are external, USB disks, this may be more challenging.
3. Make sure the currently logged-in-user has full permissions on the folders watched, and their entire subdirectory structures. This is also a very common cause of issues like this.
If none of those turn up anything, then I'd probably also do:
4. Running the Windows System File Checker. It should
always come back clean, and doesn't take very long to run.
5. If the disks are connected via USB, checking your computer for
new platform drivers is probably worth the effort. If it is an Intel-based computer, this should be simple. Also, if they're connected to a third-party USB chipset (as was common with many early USB3 ports), these are notorious for disconnects, hangs, crashes and other hard-to-diagnose failures.
Each of these items is covered in the
Troubleshooting Disks guide (the drivers thing through a link, but the rest right in the article).
If you get through all that, and
everything comes out clean (and you're sure the system itself has no nasty malware lurking), then (and only then) is it worth investigating the "really bad case": that actual data on the disk may have become damaged beyond repair. This is
very uncommon if there is not a hardware failure (which is why I suggest doing the disk health checks first), but it
could happen.
There are other things we can check if all of that checks out too (conflict with anti-virus would be my next best guess). Still, though... Let's hope that it is a filesystem error. Or, if hardware, that the disk's "automatic doctors" can detect the damage and restore the data through its block management wizardry (or, at the very least, give us a clue where to start).