This may not be totally helpful but Orion with patch manager is near worthless. I would not even attempt to look at or use anything in Orion with PM, just stick to the MMC
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I've noticed the same thing. However, it seems to get caught up somewhat once the SCCM inventory gets updated on the endpoints.
If you have right-click tools installed on SCCM you can always manually kick off a 'software updates scan cycle' on the SCCM collection(s). My environment is only about 1/3 your size, but you could still probably run it against the all-systems collection and have it finish in 15 minutes.
In this situation, it was actually that the client had disabled WSUS reporting when installing SCCM. Updating that and then running some new inventory jobs got everything straightened out.
You can also configure whether to create WSUS reporting events on the Synchronization Source page of the wizard or on the on the Sync Settings tab in Software Update Point Component Properties. Configuration Manager does not use these events; therefore, you will normally choose the default setting Do not create WSUS reporting events.