Regular dynamic menus should work with MySQLi... just not Dependent Dropdowns.
The interface that is opening for you is the standard Dreamweaver one, and not the one that is supposed to open that we created and install with MySQLi server behaviors. (image attached)
I'm thinking that maybe you need to reinstall MySQLi server behaviors. Can you send me a copy of the page you are working on? I can try to reproduce to see if it is something about that page.
Also how are you opening that interface? From the Server Behaviors panel, or from the Properties panel?
You might also try clearing the winfilecache .dat file. That will often solve odd issues that are inconsistent like you are describing.