Is the alert that is triggering a reboot alert? There is a known bug with 10.1 that will trigger false reboot alerts, but it is fixed in 10.1.2 (which is a release candidate status right now).
If it isn't what is the alert on? It shouldn't re-trigger after a reboot of the orion server.
Contracer, you should see 10.1.2 in your customer portal, which likely fixes this issue, based on your description.