Hello,
I have indeed been presented with one other case of our Toolbox program stating Windows Update has not been run on the PC. This issue arose after the client had installed both KB4015438 and KB3150513. From what we were able to gather it does appear that a recent batch of Windows Updates will configure the update history differently, causing monitoring programs to view the system as a "clean-slate", thus assuming the PC has never been updated.
As far as it returning a message stating system restored was disabled it could certainly be originating due to a similar reason, but this is not something that is a known issue.
It appears now that Toolbox is no longer giving you incorrect information if I am understanding you correctly, and we will hope the issue does not reappear.
-Dan R.