Shutdown the host properly and report if those VM boots. Try to disable/enable power on via Xen Orchestra, there's an issue in XCP-ng Center with this setting.
You can also passtrough multiple devices. If you wanted to passtrough another device at 00:19.0 just append it to the parameter.
[root@xen ~]# xe vm-param-set other-config:pci=0/0000:04:01.0,0/0000:00:19.0 uuid=<vm uuid>
@Otis2772 Where is your time synchronization coming from? Time differences can be caused by a slew of things including power settings (VM or not), CPU availability, networking connectivity, etc. Are they all the same OS or different OSes?
I am back to the office and I am troubleshooting different settings and connection setups. I appreciate all your input. The issue is configuring the right NIC0/NIC1/WAN/ and LAN. Once I am done I post my setting. Thanks again for everyone.