I was struggling to get this working on 2.0.1 also after a migration. It seems that Christian provided the answer and that you need to have both settings:
 
     $Self->{'Ticket::NumberGenerator'} = 'Kernel::System::Ticket::Number::AutoIncrement';
     $Self->{'Ticket::NumberGenerator::MinCounterSize'} = 5;
without the second setting it will not work and will default to a date generated number.
 
It looks like a documentation fix is required to add this and the docs also say that AutoIncrement is the default which it isn't
 
paul....