Gimp GIMP Redux: The Bug

In a rough attempt to give GIMP one more chance before I take a 12 gauge shotgun to it, I have used it in a pair of my most recent projects and I have found exactly what happens. Concerning my earlier ballistics of GIMP and how it has reduced my XCF work-in-progress files to one layer, GIMP has done it yet again. It had affected every single XCF file on my computer internal hard drive to one layer; again, including the XCFs I have not touched in weeks. In my dA ID XCF, I had used "copy visible" with a rectangle tool from a xcf file and made a new GIMP image with "create from clipboard. Saved the new image, saved the XCF (without the layers merged), and closed GIMP. Opening it a few minutes later to find the original XCF file has been flattened, along with every other XCF. I have rebooted my computer thinking that will accelerate the mysterious fix that it did the last time the XCFs merged, and it didn't...so I have to wait a day like I did before, before I go completely mad.

I. Am. Not. Happy. This bug will cost me everything to consistently make commissions once I can. I need a better paint program.


EDIT: I will never make sense of computer logic. I have no idea what processing task is responsible for it, but I have found the exact steps which causes the bug and fixes it, and wondering if anyone else who has used GIMP before (version 6.2, on currently Windows 8.1) had this same...discrepancy.
     To happen: In XCF file (A) with 3+ layers, use Rectangle Tool to highlight, Copy Visible, and Create --> From Clipboard to make new image (B). Save (A.xcf, 3+ layers) with layers separated, close. Save (B.xcf), close. Reopen (A.xcf), find layers merged. Open dated (C.xcf, 2+ layers), modification at least 3 days old,* find it merged.
    To restore: Create New (D.xcf, 3+ layers), save (D.xcf, 3+ layers), close. Open (A.xcf), ** (C.xcf), and (D.xcf), find all aforementioned files restored to correct layers.

* I was using an xcf file that didn't have modifications for at least a month.
** (B.xcf) will have one layer when it saves because of Create --> From Clipboard

Hopefully this makes even some remote sense. I'd love to make a video of something like this to show off this bug to GIMP.