Well, clearly a fresh install on an empty disk will rid you of this problem.
However, you may be curious as to what's going on here. To this end you need to look into the Security logs in the Event Viewer.
However, after suggesting to look at the logs, I have realized that you need to enable logging access to the folder in question, otherwise you'll see nothing. To do this you must enable Audit Policy in the Administrative Tools -> Local Security Policy -> Security Settings -> Local Policies -> Audit Policy. The point you want to enable is the Audit object access. Since we are looking for something that actually creates the folder, we would look at Success events (i.e. when something successfully accesses the folder). Once the Auditing is enabled, go to your folder in Windows Explorer, right-click and choose Properties-> Security -> Advanced -> Auditing. There you select the user name who's access will be auditing. Choose the appropriate username, reboot, and look in the Security logs in the event Viewer.
A word of warning - these audits may generate loads of log entries. Basically that depends on how often the folder is accessed. I would suggest to try your current username first. If it's not "you" who's accessing the folder, try others, like System or Trusted Installer.
Finally - this does not look like an easy task. You decide whether you want to know the origin of your problem badly enough and whether this is worth your time and effort. After all you may always re-install Windows. That process is rather quick by itself. What's time-consuming is to apply all your personal settings and install your software. How long this may take depends on how you use the machine. However, I would not recommend any sort of automated transfer of settings and personalization - you might end up with the same problem.
