I haven't used XenServer so I can't answer specifically, but have you tried running a bare Ubuntu 12.04 install on it to see if you have the same problems? It seems like stability issues would have more to do with the OS than anything installed within the OS.
Matt
Has anyone had any success running the latest version of SecurityOnion on XenServer? If so, what is your recommended build? I've been having all kinds of stability issues on both the client and the server. I've got a relatively simple setup that is primarily aiming to just run Snort and Snorby.
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I am in the process of building a Xenserver lab with SO sniffing everything going out and in on the inside interface of my pfSense VM. My problem is, I can't find a way to mirror traffic form one virtual port(inside of pfsense) to the SO sensor interface. The ESXi guys seems to have an option (http://www.forwardingplane.net/2013/07/building-a-secured-network-in-a-box/)
I would be very glad if you help me out here.