Today I added a new meta box to the admin of a template and rearranged the meta boxes on the page to be in the proper order. After saving the page the meta boxes that I'd rearranged disappeared and no longer load into the page. They aren't just hidden, but they don't load at all.
I noticed I can duplicate this issue by moving meta boxes. Any of them that are rearranged fail to appear or load on the next time the page is loaded.
I undid all my code, but am still having this issue. I have no idea how long this has been an issue because I haven't rearranged meta boxes in a long time.
For anyone that may be having an issue like this check to see if you are using the "Meta Box Columns" plugin. If so, make sure all your columns add up to 12 on each row. If they don't you'll have a bad time.
After reviewing the 40 meta boxes I've created on my site I found that the very last 3 meta boxes were set at 6, 6, and 6. I was able to fix this by changing that last 6 to a 12.