That’s the first time I’ve heard of that issue. I tried searching to see if others had this issue, but nothing came up.
I just tested ( on this site) by deactivating the Yoast plugin, but the Genesis SEO settings showed up normally as they should, and everything seems to be working fine. I have no idea what’s going on with your site.
On the page where the SEO settings are supposed to show, I did have to Open the “Tab” where they usually are….do you see a tab that’s unopened perhaps?
Also, if you go to a Page Editor (for an example) click the “Screen Options” at the top of the screen and make sure the Theme SEO settings checkbox is checked to show – http://i.imgur.com/BPXwKMl.png
Double check again that Yoast is deactivated before attempting the above steps and see if that works. If it doesn’t then I have no idea what it could be. I actually just started using Yoast a week ago so I’m still learning it at the moment.