Hi David,
If you added the field using AET, the wizard should take care of writing all he necessary BOL/Genil APIs.
Maybe there was a problem during the field generation? You could double check the field properties to see if you made is read only somewhere, or just try creating another field to see if the problem persists.
I don't think you need to do anything in Genil after using AET.
Another possibility could be if there is a BAdI implementation that's rejecting the field values. You could potentially look into order_save BAdI implementation perhaps.
If the value is there in your setter, try debugging deeper to see where it disappears, that could give you some idea on what's going on.
Hope this helps!
Parul