I have similar problems with the latest code of the free tftp server (10.4.0.14) on Windows 2008 server. I have 25 Cisco switches that copy security files to the tftp server all day long. The tftp server will be working fine, then I find the files are no longer being copied and the tftp server log shows that my security directory in the tftp root can not be found. At this point the tftp server has converted back to the default path instead on pointing to our D: drive.
I have not determined what may trigger this behavior yet, but I believe that the tftp server service may stop. I have windows 2008 server set to restart the server if it does stop. This may be when the tftp root path changes back to default.