I haven't talked to Skuzzy about it; the explanation given for the rejection seemed clear. All 10 skins had rejection messages basically identical to one of these two:
Reason for rejection: April 30, 2015, 6:18 pm: Many details of the skin were not properly corrected after resizing the skin (pixelation)
Reason for rejection: April 30, 2015, 6:20 pm: Some of the skin details were not properly corrected, after resizing the skin from 256x256.
I can see the pixelation, most evident in the exhaust manifold stack at top right in the skin map below:

I do look over the skins offline very closely, in multiple light conditions and from many different angles. Literally, I've spent hours panning around in external view, zooming in and out on these skins, making sure panel lines line up, control surface edges are correct, etc. I just never noticed anything wrong with the manifold texture. It's probably true that since it was a default texture and one that I had not changed, I wasn't scrutinizing it like I was other aspects of the skins.
Here is a closeup of the default Ki.61's exhaust manifold:

And here is the close-up of one of the skins I submitted:

The pixelation on the manifold that is so obvious in the skin bmp file just doesn't seem very apparent to me in the game, even on close inspection. I don't know how to explain the rejections, unless they didn't look at the skins in game, and only reviewed and rejected based on the bmp files?
I think it's unfortunate to have the skins rejected so close to the skin release date. If I had even one more day I could fix them and resubmit (assuming I figure out how to correct the pixelation, or someone tells me what to do) all of the skins.
Man, I can't tell you how much I was looking forward to having some new skins for the Ki.61 in game!