Hey Jon,
There's an agent side patch for collection of System Updates by the AM agent:
r12.9 GA: T5IZ292 (Inventory collect timeout on age)
r14.0 GA: T5IZ342 (System update inv collect timeou)
If I remember correctly this was fixed permanently in the SP1 release, and forward. Root cause was a timeout within the AM agent for waiting for the WMI/wmic command to return the completed list of system updates. The timeout was too short, hence the data would get missed from being collected on every endpoint.
You can open a support case to request the patch if you're on either of those versions.
-Brian