For all systems? What version of ePO? Do all these systems have the same policies assigned? If 100% sure on VSE as the cause, what does the VSE policies look like?
Really any further information your willing to share would help the community.
I have ePO 4.6.6 with almost a 100 users and only 3 people (all recent installs) have said they get this message. I haven't changed a thing on the system for sometime, currenty VSE 188.8.131.52 (patch 3) and Agent 184.108.40.2060. I have also loaded up a couple of new computers without getting that message. We do put a ton of software on our computers.
I finally watched it happen and it is VSE 8.8 as the problem with the Agent 4.8.1500 is doing the reboot request and the reason is that the patch 975 can't load. Actually none of the patches or hot fixes will load on one PC. I uploaded VSE patch 4 to the ePO and that installs over 3 easily and automatically on all of the other computers. But on the 3 machines with the "reboot request", I can't get any thing to load. I've uninstalled repeatedly. Tried and failed to install patch2 manually. I've tried all the possible fixes I could find for patch 975 errors.