Okay, so I have some answers, if not the final answers.
First, you’re correct, if I remove the cover from the compile (I actually removed it from the entire Scrivener file), it then begins at the correct place (start of chapter) on all the devices I have. That is, without a cover, if I use “Send to Kindle” it starts after the front matter on a Fire, Paperwhite, and Kindle for iPad. (It always worked fine in Kindle Previewer.)
Second, I did some checking and it is recommended that you don’t include the cover in your text file when you upload to KDP. The cover should be loaded separately. Not only that, but I went ahead and did it myself. The complied text file without a cover, loaded the cover separately, and put the book up for sale. Amazon added the cover and the books now up for sale.
You can check it out here: amazon.com/dp/B00VTQ9D0M
So happy ending? Not really. Unfortunately, for some reason when Amazon put the cover back in, it doesn’t start after the front matter, it (generally) starts at the table of contents (on iPad for Kindle and Paperwhite). Worse, the glitch reappears when I check it on my Kindle Fire.
Conclusion: yes, there’s some kind of bug in Kindlegen or something, and it’s almost surely on the Amazon side.
So what to do? Probably it’s just something that has to be lived with. I would personally recommend everyone compile without a cover for mobi and upload the cover separately. I’m also going to check with Amazon support to see if I can get the start page changed by them. I’ll let you know if that works.
(By the way, I did try compiling stock ebook and the glitch didn’t appear. And it didn’t appear when I just added my cover (so it wasn’t something in my cover itself). It did, however, reappear when I added in the text of my original novel (which I had exported into RTF). Something in that. Length of text? Something in the text? I didn’t fully debug it all, because I thought I’d try uploading to Kindle for sale. And since Amazon reintroduced the bug, it kind of doesn’t matter.)