Keep in mind that scanning any HKCU value will potentially have unpredictable results in inventory. the issue being that the inventory scanner may execute when a user is or is not logged on to the system. In the event that the latter scenario occurs HKCU will be unavailable at a time when a user is not logged on, and will not return the data to inventory. This might cause the data to drop out of inventory on a device. Also, if the inventory scanner is running in system context HKCU doesn't reflect the actual logged on user's user hive, but rather reflects the system's user hive, which might not even contain the data or may have different data. I would potentially suspect the former not the latter in your scenario.
a suggested solution for unpredictable problems with an HKCU value.. If you can do this, devise a way that when a user logs on, a script executes (maybe GPO or logon script), and very quickly copies this HKCU value to an HKLM location. (Make up some special key for your custom registry collection) Then design the custom data entry around that location instead. This way your inventory scan will always succeed in getting this data.