Although I have many system utilities software installed on my device, I like Reg Organizer the most, I feel it has good useful utilities, I was contacting the developers for couple of months now to report issues, and they were very kind and helpful.
I think this message related to the uninstaller, when there are some entries are not same to remove or not related to the removed software alone like file extension.
You can continue using it after trial period end, there are no limitation, it will notify you that this is a trial version just like WinRAR do.