Windows 7 Missing Files in Folder (Properties vs. Explorer)

The third party software has either been used continually with these files for years without a problem (ThumbsPlus) or hardly ever (AC Browser Plus).

There are no DRM issues with these files; they're all .jpgs. They were perfectly accessible a few days before the problem happened, via both Windows Explorer and ThumbsPlus.

They have essentially all been moved to the current directory with ThumbsPlus, an image managing program. Since ThumbsPlus can access files in the directory that aren't showing up in either Windows Explorer or AC Browser Plus (the files that is has created a thumbnail image and hence its own directory information for), it seems very unlikely to be the problem.

There's nothing else in the folder, no pointers, etc. It's as simple as could be.

Since everything else on my hard drive and directory system is working perfectly, the most parsimonious explanation is a single point of data damage that happens to be in the MFT for this directory. One point of damage is more credible than two. If this were DOS, I'd have already fired up my hex editor, examined the directory, and fixed the damage. But I don't even know where the directory information is located (all I've been able to gather is that it's called the MFT!) nor how it operates. That the file list is truncated alphabetically has to be a clue. Is the file list dynamically or periodically re-alphabetized to speed access? What kind of damage would cause a problem like this despite the presence of the backup / mirror copy? I need someone with a fairly intimate knowledge of the way the Windows 7 directory system operates to make sense of this.