Did you find a solution for this?
I am using 2011 SP05 and I notice the same problem. I wondered if it is a bug in this version.
This ia a Windows 7 compatability issue. Windows 7 does not allow modification of a system folder. The Templates directory is inside the program folder and is trying save a template there. There is no way with this version of FlowSimulation to modifiy the template folder locoation. To fix this problem you have to run SolidWorks as an administrator. Go to C:\Program Files\SolidWorks Corp in window explorer and right click the SolidWorks.exe file and select properties. At the bottom of the 'Compatability' Tab is a check-box for 'Run as Administrator'. Check that box. Create a new short-cut for the desk-top and then update any quick launch icons with this now short-cut. When you start SolidWorks with this short-cut it will bring up a dialog box. Select yes. You are now running SW as admin and you can now save templates.