Policy settings being "refreshed" or deleted from registry

I am running windows 7 & 2008 R2 computers in my network.  I use secedit to push out settings to the following registry areas during the OS install:

HKEY_LOCAL_MACHINE\Software\Policies
HKEY_LOCAL_MACHINE\Software\Microsoft\Windows\CurrentVersion\Policies
HKEY_CURRENT_USER\Software\Policies
HKEY_CURRENT_USER\Software\Microsoft\Windows\CurrentVersion\Policies

After several months, these settings are deleted by some process.  This only happens to a small number of computers in our domain.  I am wondering what would cause group policy to delete these keys and "start over"?  Is there something that I am unintentionally doing to make Windows refresh all of the group policy settings?

Thanks.