Welcome to the Circle Dock Forums here at donationcoder.com
My apologies that you ended here because of issues with Circle Dock.
Admittedly I have not had this issue, nor can I reproduce it, so I can not develop a log file to check stuff
Of course I am also in Windows 7 64bit.
I unfortunately may have to let Markham in on this one, as I am at a loss as to how to proceed.
I am going to suggest a simple test to see if there is something screwy.
Start Circle Dock with Administrative Privileges and then shut down to see if you have the same issue.
apparently there is an issue in Circle Dock's shut down sequence.
Circle Dock writes to the XML files during shutdown, my guess is that something is getting hung up here, but I could not say why, just a guess.
Do you have a standard install?
Or have you installed to a different location or portable media?
Additionally; What Antivirus are you running, if any?
Let us know and I will help to figure this out as I can