are you by chance using provisioning services for your XEN environment? We've had some inconsistencies with vMotion and XEN Desktops. Our environment is set to fully automated for DRS, but we don't have a lot of DRS events. We haven't had an issue with the XEN desktops go offline, but there is a "pause". That is one of the downfalls with VDI... any inconsistency in the environment will be seen immediately because you have users working on the VDI VMs all day long.
I don't know what the exact fix is, but i'll see what our Citrix folks have done to try and reduce the timeouts.