This thread saved me a lot of time and effort so I thought I would give something back. 
I also experienced the same issues with the link not coming up in Windows 2012 R2. 
I have Two 49Y4202 directly connected via a 5 meter Twinax DAC passive cable.

Here is a small and very, very basic batch file you can run at startup to enable the link . It's not optimal but it works.

Prerequisites
Install the OneCommand Manager GUI on both windows 2012 servers (Link as of 9/29/2016). 
You can also install the CLI version. I tested this on the GUI version. It should install to c:\Program Files\Emulex. 
The executable we need is located in c:\Program Files\Emulex\Util\OCManager>HbaCmd.exe. 
I would also highly recommend reading the Windows CLI PDF located here. It has details on all of the commands you can run. 

Get the Mac address of each port by entering the following into an elevated command prompt. 
Change x.x.x.x to the ip address of the Onecommand server. 
If you run this command locally it will tell you to remove the h=x.x.x.x. 
Obviously you need to do this on both sides of the link in order to collect all 4 Mac addresses. Assuming you have two 2 port NICS.

c:\Program Files\Emulex\Util\OCManager>HbaCmd.exe h=x.x.x.x listhba

You should see something like this:

Manageable HBA List

Permanent MAC : 00-00-00-00-00-01
Current MAC : 00-00-00-00-00-01
Flags : 00000710
Host Name : xxxxxxxx
Mfg : Emulex Corporation
Serial No. : xxxxxxxxxxxxxxxxxx
Port Number : 0
Mode : Initiator
PCI Bus Number : 2
PCI Function : 0
Port Type : NIC
Model : 49Y7941
Discovery : RM

Permanent MAC : 00-00-00-00-00-02
Current MAC : 00-00-00-00-00-02
Flags : 00000710
Host Name : xxxxxxxx
Mfg : Emulex Corporation
Serial No. : xxxxxxxxxxxxxxxxxxxx
Port Number : 1
Mode : Initiator
PCI Bus Number : 2
PCI Function : 1
Port Type : NIC
Model : 49Y7941
Discovery : RM

Create a batch file such as enable_10GB.bat or whatever you want to call it.
Now that we have the MAC address of each port on each side of the link we can build the script.

Paste the following code into the script and save it as a .bat file You can leave out the rem statements if you desire.

@ECHO OFF
cd c:\scripts\emulex\
Rem "Make sure you have installed onecommand on both windows 2012 servers"
rem "To get the mac adress of each port run c:\Program Files\Emulex\Util\OCManager>HbaCmd.exe h=x.x.x.x listhba. 
Replace x.x.x.x with the ip of the remote onecommand server. Note the Permanent MAC of each controller port"
rem "Replace the 00-00-00-00-00-00 with the mac of the port1, port2, port3, port4. 
The 0 at the end disables the port and the 1 enables the port"
"C:\Program Files\Emulex\Util\OCManager\hbacmd" SetPortEnabled 00-00-00-00-00-01 0
"C:\Program Files\Emulex\Util\OCManager\hbacmd" SetPortEnabled 00-00-00-00-00-01 1
"C:\Program Files\Emulex\Util\OCManager\hbacmd" SetPortEnabled 00-00-00-00-00-02 0
"C:\Program Files\Emulex\Util\OCManager\hbacmd" SetPortEnabled 00-00-00-00-00-02 1
"C:\Program Files\Emulex\Util\OCManager\hbacmd" h=x.x.x.x SetPortEnabled 00-00-00-00-00-03 0
"C:\Program Files\Emulex\Util\OCManager\hbacmd" h=x.x.x.x SetPortEnabled 00-00-00-00-00-03 1
"C:\Program Files\Emulex\Util\OCManager\hbacmd" h=x.x.x.x SetPortEnabled 00-00-00-00-00-04 0
"C:\Program Files\Emulex\Util\OCManager\hbacmd" h=x.x.x.x SetPortEnabled 00-00-00-00-00-04 1

Copy the batch file to wherever you like. IE c:\scripts\emulex\.
Create a Basic Task scheduler task
Choose When computer starts Task Trigger
Choose Start a Program for the Action
Browse to wherever you stored the script. c:\scripts\emulex\ in this example. Leave arguments blank
Click the box to Open Properties dialog for this task when I click finish
Click Finish
Enter the username\password of the user to run the batch file. The user has to have admin rights.
In the advanced Settings area click the Delay task for up to (Random delay) and change the setting to 1 minute. 
This will give the onecommand server time to start. Hit ok.
Power off the server and then turn it back on. The link stays up for me if I simply reboot either of the servers. 
It doesnt' come up only after a power off of either server. After one minute the link should come up on it's own.
Do the exact same steps to the 2nd server. Be sure to swap the IP's and mac addresses.

The other cool thing you can do is install the onemanager on your desktop. 
Change the script above to include the h=x.x.x.x for all of your servers and then run the script from your desktop. 
This will disable and enable all 4 ports. This is how I initially tested the script. 
Read the manual, there are some cool security features you can enable also. 
For obvious reasons, you probably don't want anyone on your network to be able to run these commands. In my home lab it's not a problem.