I confirm when removing a PCIe* video card, any of the 3 video ports (up to two) on the back of the board should start working automatically. Hence, based on the troubleshooting you've described, I'd suggest trying with the most current 0057 BIOS (click here).
Note: Once the update is done, please, restart the system into BIOS and proceed as follows:
1. Press <F9> to restore BIOS default settings.
2. Reset any customized BIOS settings.
3. Clear all DMI event logs by setting the option to "Enable", which is located in the Configuration/Event Log section of the BIOS Setup utility.
4. Finally, press <F10> to save the new settings and reboot the system, and test.
I was having the same issue. I just updated to BIOS 64 and the issue is gone. What I did:
1. Before install, load BIOS defaults
2. Download BIOS file to fresh USB stick
3. Hit F7 on reboot
4. Select and update BIOS
5. Load BIOS defaults
6. Remove add-in card
7. Reboot and load BIOS defaults again
Now it seems to work.
Didn't test both outputs though, but at least one of them is confirmed to be working now.