Thank you Qavion and Golden Rivet.
In our procedures we do not move the Flap Lever during Alternate Flap extension. There seems to be a difference in the procedures between older 200 and newer 300 series aircraft. On earlier 200 and 300 series aircraft the Authrottle will disconect once you select the Alternate Flaps to Flap 5. On newer aircraft there is no mention in the QRH to disconnect the Autothrottle and the Autothrottle will not disconnect with Alternate Flap selection. Could it have any thing to do with the FADEC computer?
Regards