I too have seen problems related to created file permissions on Windows 2008.I believe these permissions problems are related to User Account Control (UAC).
By deafult, when you are browsing around the file system using explorer, you are doing so without the "Local Administrators" group token. You may see an example of this when trying to open a folder and encountering a UAC yes/no pop-up--answering yes will add your specific userid to the permissions for that folder.
When you create a file in a folder you created from scratch, say an app or sometimes a new configuration file, it might only give your specific userid permissions on the file and forget to also allow other local admins or system accounts (which splunk may be running as).
My practice has been right-clicking on a cmd.exe shortcut and choosing run as administrator. I then navigate to directories using this prompt and manually typing "notepad filename.conf" to create or edit files. This starts notepad with permissions needed to save the file appropriately.
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