Should be fixed now.
There have been few changes in the classes :
classes/jmodel.item.php
classes/jmodel.list.php
classes/jcontroller.php
AND :
In all _new() functions of your controllers.
Yop, it was not easy to fix this but now is much more better.
I am really soooo sorry to still have a not stabilizated generator. It adds you a lot of work every time to update the changes. I am profundly aware of this and it will be much better after the v2.0
All theses details here are already solved in the 2.0 version.