Seems like some rather strange behaviour - support should be able to help you with what the actual reason behind that happening is.
Off the top of my hat the first solution I could think of is to push out the regular agent via GPO and then push out the agents registry keys which actually include all of the options you set during configuration.
You can find those in your DW root directory, the file that stores them is called DWRCS.reg and looks something like this:
[HKEY_CURRENT_USER\Software\DameWare Development\Agent Configuration\Mini Remote Control Service]
[HKEY_CURRENT_USER\Software\DameWare Development\Agent Configuration\Mini Remote Control Service\IP Filter]
"Enable Filter For Remote Control"=dword:00000000
[HKEY_CURRENT_USER\Software\DameWare Development\Agent Configuration\Mini Remote Control Service\Settings]
"Force Direct Connection"=dword:00000000
"Remote Connection Availability"=dword:00000001
"Notify On New Connection"=dword:00000001
"Notify On New Connection Timeout Value"=dword:0000000f
"Notify On Disconnection"=dword:00000000
"No Notify Sound"=dword:00000000
"Notify Dialog Caption"="DameWare Mini Remote Control"
"Notify Dialog Text 1"="MRC Notification"
"Notify Dialog Text 2 Remote Control"="MRC Notification"
"Permission Required Also When Locked"=dword:00000001
"Center Permission Dialog"=dword:00000000
"Permission Dialog Set Focus On Decline Button"=dword:00000000
While this isn't exactly a solution it might be a workaround worth considering.
Thank you for the information regarding the registry key. I will give that a go.