Hi,
I had this exact problem and couldn't find anywhere that seemed to specify this setting. I don't know if there's a better way of achieving this via the software itself, but after comparing the "local" administrator account's registry with a new domain account's I created to access our network resources, there seems to be an extra setting:
Under HKCU\Software\SAMSUNG\MagicNet_Client\Pro there's the key "StartUpProcess"
On my domain account this was set to "0" on the local account (that worked) it was set to "2".
When I matched the setting on my domain account, the software automatically runs when it starts.
As I say, I imagine there's a nicer "software" way of doing this, but as I couldn't find it, I went for quick and dirty!
Hope this helps someone.
Cheers,
SputterOut