I know this is an oldie but goodie but I assure you it is not the AutoShareServer key. We have a Forest with several OUs. In OU 1 we have 2008 R2 servers and some 2003 Servers. Their AutoShare settings remain correct. In Blocked Inheritance OU 2 we have several 2003 Servers and an XP Workstation (I know...I know egads XP and the end of life around the corner). In OU 2 on either reboot or restart of the server service the C$, D$ ADMIN$ shares are deleted. I have verified the AutoShareServer and Wks keys in all ControlSets and they are set to 1.
I am quite certain given our environment that its not a malicious app, especially since its conveniently attached to only OU2 systems. Recreation at the CMD line and repeated reboots resolves nothing. I have scoured every GPO and there are no references overriding the setting (but as I noted the setting remains set as it should be). I have performed GP Resultant sets on the affected systems in an effort to determine whether anything obscure is creating the problem and nothing appears out of the ordinary. I saw a post pertaining to iSCSI having these issues but iSCSI is not a consideration in this environment.
With all of that said i am out of options and all my scouring technical forums has produced no other options. If anyone out there has seen this and has an unattempted solution I have not mentioned above I am open to ideas. Thanks again...