MNSU,
The process you are speaking of is automatic update, this can be turned on and off in Control Panel -> Altiris Deployment Server (32-bit) -> Options -> Transport and uncheck Automatically update clients.
The clients that are not running will update later once they come back online and check back in with the console.
MP4 has fixed a lot of issues with GSS 3.1 but there are still a few known bugs that we are aiming to fix in later MP releases. Please see the below documentation for release notes for MP4
https://support.symantec.com/en_US/article.DOC8558.html