I have a similar issue. We have Windows updates disabled, and Kaseya says there are no missing patches & no reboot required. When you go into the server Windows update says that there are patches pending and a reboot is required to install updates. Where on the machine is the reboot required message in Kaseya coming from and which one is correct?
Are you approving patches by Patch policy?
If you deny patches but windows updating is still turned on, it will show you all the patches you denied in Kaseya.
I know you said you disabled windows updates, but when you do a manual Windows update on the server i think it might turn it back on. The patches you are seeing are the ones denied by Kaseya (or at least that's my theory anyway)
I'd think its safe to ignore the symptoms and either trust Kaseya, or don't. I know that with some strict rules approving by patch policy, i hit well about 90 percent patching every single time and i have never had a negative impact, my customers have never had such up time. WSUS on the other hand, not so much.