Rebooting the computer resolved the problem.
In the process of installing the LabVIEW Runtime and the System Configuration module, the NIPM repeatedly requests that the computer be rebooted. I was operating this computer remotely, through GoToMyPC, and I may have inadvertently missed one of the requested reboots. This might have left NIPM's records reflecting that a previous update was still in progress.
Thanks to Scott_Richardson for the clue!