Το έλυσα. Για κάθε tableadapter, είπα στο ontablenewrow να φτιάχνει ένα guid και έκανα override το endedit. Τώρα παίζει άψογα αλλά... παράξενο δεν είναι ?

using System.Data;
using System;

namespace WindowsFormsApplication1 {  
    
    public partial class testDataSet
    {
        partial class masterDataTable
        {
            protected override void OnTableNewRow(System.Data.DataTableNewRowEventArgs e)
            {

                base.OnTableNewRow(e);
                ((masterRow)e.Row).masterID = Guid.NewGuid();
            }

            public override void EndInit()
            {
                base.EndInit();
                this.TableNewRow += delegate(object sender, DataTableNewRowEventArgs e) { };
            }
        }

        partial class childDataTable
        {
            protected override void OnTableNewRow(System.Data.DataTableNewRowEventArgs e)
            {
                base.OnTableNewRow(e);
                ((childRow)e.Row).childID = Guid.NewGuid();
            }

            public override void EndInit()
            {
                base.EndInit();
                this.TableNewRow += delegate(object sender, DataTableNewRowEventArgs e) { };
            }
        }
    }
}