Two things on this one.
1) all unmodeled data(custom data) is blocked by default in LDMS 9. Please see Custom Data is not Entered - Using the Unknown Items Inventory Tool
2) you need to be careful with HKCU keys- they will only show up in the inventory scanner is initialized by a logged in user. If an inventory scan is ran as a scheduled task- it will run as local system- it will not pick up HKCU keys as Microsoft does view the localsystem as a user account. Also once that scan is uploaded it will remove any HKCU data from the record, as part of the update process.
Turned out to be the first note you mentioned. I was not aware of that, and I don't think our LANDesk rep was even aware of that. Yeah, I know HKCU is pretty limited on what you can do with it. That is good to note, though. Thanks again!