Welcome to the world of managed installations. If you already have the sccm side set up correctly, just build a new AIP and sccm package when the updates come out then push it down to the clients. I disable all local updates in the customization wizard since they could saturate the network connection when an update is available and prefer to manage updates locally using SCCM. I have not run into the problem you describe since we don't use the local update client.
I'm having a similar problem. Previously we have created a new deployment package for LUP every time adobe releases an update for Reader, but this is somewhat time consuming to keep up with the most current version...TheITGuy13, can you explain in further detail what you did with the Adobe Customization Wizard XI tool, I haven;'t used it before
View the Wizard doc for Win here: http://www.adobe.com/devnet-docs/acrobatetk/.
It simplifies most common configuration tasks.
10.x and later installers are cumulative so intermediate security patches never need be applied except for the last one (if any). Updates average about 4 per year.