In AGS 10.0 I shared the C:/arcgisserver folder, and now my apps and rest endpoints will not display any of my cached services. I can view them fine in ArcCatalog however. I can build new caches but they are only visible in ArcCatalog.
AGS Site seems to be battling Windows Server for permissions. Here's how my permissions are set up.
Name: Permission Level Admin Owner AGS SOC Read/Write AGS SOM Read/Write User Read/Write