I haven't heard of this issue before due to our program. Do you get any indication of which application is producing the error? If there's no indication of that, the only way to figure out which application it is, is to go to Startmenu -> Run and type in msconfig. In the new window that appears you should have a tab called Autostart. There should be a list with all the applications that start when Windows boots up. You then have to disable everything in that list except for one application, then reboot your computer. Keep enabling one at a time, and when the error message comes back, you'll know that the last program enabled will be the one with the issue.
However, our program makes a backup every time a registry clean is done, so you could revert back to how it was before the registry was cleaned. That option wont reveal what caused the issue though.