10.8.2 keeps repairing system folders which ruins my version of English.lproj. Does anyone have and suggestions to fix this?

I work for the Eastman School of Music's Computer lab. We are testing out Mountain Lion with the intention to move it in to our labs in December. Typically we create a user template by rsyncing our changes to the standard template to /System/Library/User\ Template/English.lproj/. We use iHook to delete the Lab User when people log out, and when new people log in the template from /System/Library/User\ Template/English.lproj/ is used to create the new Lab User. The problem is that Mountain Lion seems to have a self healing aspect to it so it removes the changes we make when we rsync. When our Lab User logs in now they get a default apple desktop instead of the one we create. We have a lot of apps that we want in the Dock and we need a way to keep our changes to the Lab User template.
Is it possible to make OSX 10.8.2 stop fixing our changes to /System/Library/User\ Template/English.lproj/? Or is it possible to get our labuser to call its information from another template that OSX 10.8.2 will not interfer with? Is there some kind of plist I should be looking for that controls where OSX directs its requestes for how to set up new accounts?
Thanks,
Stuart-

It turns out that the solution was right in front of my face. Our old script was wipeing out the caches from the computers. When I commented that out of the script everything went back to normal.
Stuart-

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