It looks like it's an eBay issue that at the moment can't be fixed unless you upload the intended gallery photo to one of the variations, which would then confuse buyers, I think. 

I hadn't noticed this happening until this thread, but can see it's affected my variation listings as well. I opened one up to edit and see if I could fix it, and the first photo uploaded to the first variation has been designated "Main photo" which is usually reserved only for the primary photo in the large section for the global images (if that makes sense). 

I checked another one and again, the first image in the global photos is designated "main photo" and then the first image in the first variation has also been designated "main photo" and that's the one that's showing up in the searches. 

I'll have a bit of a play with one of my listings that's variation but out of stock later today, and see if I can figure out a way it can be worked around or fixed - if not, it's just another tech issue we'll have to wait for eBay to get around to, I suppose. 😕