I'm using version 22.214.171.124 of AAM
Here is a screenshot of the menu I'm talking about: Screenshot
When I use the menu for e.g. the contributor role and for the submenu Dashboard I check the items akismet stats, updates, event viewer and uncheck Home and Whole Branch and then Save, the result is that Whole Branch is checked and the rest is unchecked.
The only way to achieve the access to the Home of Dashboard by the contributors is to uncheck all the items and then Save, the result is shown in the image.
It is therefore impossible to check and save individual items in the submenu's of the main menu, when you do this the "Whole Branch" item is checked, the rest of the submenu is unchecked and the result is restriction to the whole submenu for the specific role.
I tried this a dozen times, clearing cache over and over again etc... but no change in behaviour.