If you're looking at machine view it will display the latest information from any scan performed against a machine. If the console scanned it last but using a different scan template than the agent it could end up showing different results in the machine view for that system.
This might be a difference in the scan template and filtering is being used between a scan from the console and a scan from the agent.
Check these things:
-Scan template that was used to scan from the console
-Scan template that is specified in your agent policy patch task.
(Look at the difference between the two, if any)
-Are any patch or service pack groups in use? Is there a difference in what's used by the console scan vs. patch task in your agent policy?
-Ensure that 'Use replacement patches' is checked in Tools > Options > Scans in the console.
I hope that helps.