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We are specially concerned about if our users keep updating their browsers, flash player, adobe reader, java( feel free to let me know some others that are also important). These applications usually the most common entry for attack/virus.

For windows and office update, we are doing well with WSUS. But we have noticed some users disabled flash player auto-update. Any idea? Is it possible to solve the problem through GPO?

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There are a few different options I can think of off the top of my head. The easiest way would probably be to push the updates yourselves, either through a deployment project that can be tied in to WSUS or more simply, through a log on script that would check the version and update. Both require some custom setup to make work though. GPSI can also be used though it is a bit older and doesn't scale as well for larger setups.

I know we generally frown on linking off-site but there is a really nicely done write-up on more detail about this here.

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