Windows 10, whether upgraded from a prior OS or using a fresh OS install, cannot complete patch scan when server is at R9.1 and the agent is at R9.1. The patch scan will report as completed but the patch data may not report correctly.
This is a known issue that is being investigated.
The problem is addressed in VSA R9.2, which adds full support for Windows 10.
Further details can be found here - http://www.kaseya.com/kaseya-release-9.2
Kaseya VSA 9.1
SVE-3617 / #97152