I found this a bit of a gotcha, the Citrix polices in XenApp 6.0 for Disconnection timeouts are for XenDesktop only and do not effect XenApp.
To control the Disconnection timeout change the following key
HKLM\SYSTEM\CurrentControlSet\Control\Terminal Server\WinStations\ICA-TCP
MaxDisconnectionTime
This value is to 1000th/sec so a value of 1000 = 1 second
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