you may need to check-in single package Patch 3 for VirusScan Enterprise 8.7 and create or enable VirusScan patch update in an update task, not just relying on the VirusScan 8.7 repost Patch 3 install set deployment task. The agent must be checking major version only, and this could be why it does not upgrade manually installed VirusScan 8.7 repost Patch 2 product.
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At a guess, I would say that you need to check in the VSE 8.7 patch 3 package, as well as the "combined VSE 8.7 plus P3" package that you presumably already have, and then schedule an update task that is set to update VSE 8.7.
The combined package will be deployed to client machines running 8.5 or earlier by the deployment task: the update task will apply just the P3 package to machines running 8.7 without P3.
Hope that made sense
Thanks for your answer. Checking in the patch solved the problem. New machines get the correct patch and all the existing ones updated.