Generator supply not working with Automatic Changeover
Neutrals are not the same!   The factory certainly would not have wasted money on separate neutral terminals if they were not necessary.

It needs to be hooked up according to the instructions for that unit.  In my country that is the law.  Why? Because the unit is only safety tested/certified for correct configuration. A wrong configuration could be dangerous. 

It sounds like whoever hooked it up did not follow basic instructions.  Don't let them do any more work on your house!