Many people have expressed frustration with Adobe Illustrator when they try to export a layered PSD file/s. Even though they check the checkbox to export layers with maximum editability they get flattened layered files rather than multiple layers.
When you have multiple artboards in one ai file, if one of those artboards contains an object that Illustrator wants to flatten, it will also flatten the all other artboards. I find it easier to do all of my work for one project in one ai file rather than have many different files.
In my case I had 12 artboards which I was trying to export at one time as layered PSD files but all of them were being flattened. By separating all of the artboards I found that in one of the 12 artboards there was a complex vector image that used a lot of blends, and blurs and multiple masks that Illustrator would not translate into a layered PSD file.
You can use Window>Flattener Preview in Illustrator to find objects like the one that gave me trouble. In the Flattener Preview window Click 'refresh' and then select the dropdown option 'Raterized Complex Regions'. This will show you the objects that could be causing Illustrator to flatten the PSD layers when exporting.
In my case I exported all other layers and then I grabbed these objects and dragged them directly into photoshop and placed them in place manually.
Hope this helps.