When I rolled out agent 5 quite a lot of machine popped up a message saying that a reboot was required (mainly servers). The latest agent seems to incorporate a lot of new functionality and new services so I'm not surprised. Unfortunately there are some issues with the new agent and I personally wouldn't upgrade until the next patch is made available.
Could you please confirm, if the issue is reproducible, (Reboot prompt after upgrading to MA 5.0). As i tried upgrading MA to 5.0 many times but never got a Reboot prompt.
Could you please share a screenshot, and what all Mcafee Point Products are installed on the affected machine.