I am thinking SimonF is onto something with your passed thru USB controller(s).  If the ports are passed thru, they are not available from the main host.  How many iommu groups for USB controllers are available?  Are you able to just pass thru one and get your 3 port fix for HA?  If all your ports are in the same iommu group, I don't know off the cuff how to split them, but I DO believe I read it's possible.  I think you have some juggling to get it just right.  Maybe a usb2.0 header like this  could add options.

17 hours ago, SimonF said:

Looks like one of the host controllers is being removed are you passing into a VM? I would disable the usbip options if not using.

Thanks everyone for helping! 

 

I'm not sure when this happened, as I really don't recall making this change, but last night, I made a USB and moved it over to it. After the Array started, it broke again, so I started looking and found that one of my VMs was, in fact, passing this over. So, I'm the issue here.* I'm also not 100% sure why after I swapped the CPU, this happened. either way, thanks again. 

14 hours ago, Veah said:

I am thinking SimonF is onto something with your passed thru USB controller(s).  If the ports are passed thru, they are not available from the main host.  How many iommu groups for USB controllers are available?  Are you able to just pass thru one and get your 3 port fix for HA?  If all your ports are in the same iommu group, I don't know off the cuff how to split them, but I DO believe I read it's possible.  I think you have some juggling to get it just right.  Maybe a usb2.0 header like this  could add options.

yeah, he was for sure right. After doing a USB swap it broke again after the Array started. While I don't recall actually enabling this one of my other Linux VM's was getting this passed to it. I removed this and it then started working. I am a bit mad about using a USB migration to find this but at this point it is what it is. just going to make sure to do regular backups of this USB