Software Deployment

I'm trying to deploy SQL server 2008 via SCCM. I created a configuration file and get get it to install via the command prompt no problem. However, in SCCM, it keeps failing on me. I'm thinking what is failing is the dummy command window that opens up after you start installing it silently. Is there anyway to suppress this command prompt or have SCCM not care that it wants to open. A similar thing happnes with Cisco Supervisor, but SCCM opens the dummy command prompt in the background and keeps installing. I haven't tried repackaging it yet. Has anyone else had a similar problem with this? 

Thanks,

Mark