Just to clarify, the reason people are running into this issue is that max_input var. PHP by default doesn’t allow forms to submit more than 1000 post variables. This is done to prevent a obscure but devastating Denial of Service attack.
The limit appears to be ~90 menu items because each menu item has about 11 hidden form fields attached to it. The edit menu page can’t save large menus because of this. Certain plugins might add even more options which will increase the size of the form.
Another solution would be to look for a plugin with a drastically different menu editor. Maybe one that doesn’t let me drag and drop menu items, because that would greatly reduce the number of form variables. I’m going to hunt for one, because the site I’m looking at running has deeply nested pages, and we’re hoping to support more than 90 menu pages. I’ll followup here if I find a plugin that does this job.