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In Patch 3 release notes there are two sections that might involve your symptoms: "Hotfix/Patch reporting" and "Verifying installation" point is that version report only occurs if file version info matches what's in the registry. This may or may not be true for you, but I would recommend a reboot on another client (without setup.exe /forcemsp=yes, etc.) to see if it resolves the symptom. A reboot otherwise is recommended for the patch to load fully and might update the file version info (which earlier could not be done due to files could have been in use).
Thanks Mate, I have advised the customer to perform a reboot as the registry shows hotfix and version. Hopefully it should solve the problem...