In the Main Computer window, PDQ Inventory shows that a reboot is required on a machine or set of machines. Clicking the "Yes" link will give you more information about exactly what keys are flagging this reboot. This article explains how PDQ Inventory retrieves this information.
PDQ Inventory scans the registry of the target machines from a few different places to determine the reboot requirement:
HKLM\SOFTWARE\Microsoft\Updates\UpdateExeVolatile\Flags [looking for a value of 1, 2 or 3]
If a reboot of a target system followed by a Standard Scan (or any scan profile containing Computer Info) doesn't remove the machine from the collection, check the above registry entries for the corresponding value indicating that a reboot is (still) required.