Not a 100% sure on this, but LD 9 has a new feature called "Gather Historical Data", no one seems to know for sure what it does... but I have found that if I run it, it clears up a lot of patching data.
I have mine scheduled to run once per day, and if my numbers look goofy, I run it as needed. Give this a try.
Go to the Patching tool section, go to create a scheduled tab, choose "Gather Historical Data", and run it.
I am having the exact same problem. My queries some up with a fraction -- 1/4 to 1/5 of the number of installed patches showing under Security and Patch Information. Gather Historical Information (under Create a task in Patch and Compliance) is not working at the moment; but when it is I will try it. However, none of my 28 field office IT specialists have access to the 32-bit console. They must rely on the queries or reports they can access from the web console.