Hi everybody, I had the same issue with my VRTX. Port gi 1/1 kept reporting down no matter which blade I plugged in and gi 2/1, 3/1. and 4/1 worked with any blade. I called Pro Support and it turns out there's an internal KB for this issue. Dell dispatched a new midplane and everything works fine now. It takes a couple hours to tear the whole thing down and put it back together. Definitely have a tech come if you have the option.   tl;dr Call Dell. It's a factory defect, get a new midplane. 
I don't know if this is a server or network issue, but I post here anyway.. Trying to set up a Dell PowerEdge VRTX with a R1-2401 VRTX 1Gb Switch Module. But port gi1/1 insists that is in a down/down state. The OS also says not connected. What I am doing wrong? All other ports are connected fine. This is a M620 server, if that helps at all.  
PowerEdge VRTX with R1-2401 VRTX 1Gb Switch Module - cannot connect port gi1/1