Are these issues known about or is this possibly a problem with my copy?
Maybe yes, might as well not.
It may be the fault of the plugin or script. Which plugin or script you are using?
Try updating the database with each plugin or script separately, then maybe in one of them, you can maybe find a bug, which then causes problems with the database that damage to this one.
Perhaps there is any error in the PVD software.
Perhaps it would be good to impose new again, sooner you however, make a copy yet old PVD software and a copy of pvdconf.ini file and other files, then you have copies of important software PVD files, if to by may later need.