I don't use the metro screen, but I do have a 3 monitor setup, and it does affect the boot.
EasyBCD has absolutely no effect on your boot process.
EasyBCD is a Windows .NET application which only works on a running version of Windows.
What you do with it will affect all future boots, inasmuch as it has taken your instructions to make changes to the data which bootmgr will use on each subsequent boot.
If you do something with EasyBCD (like select metro), which works, then it will continue to do exactly the same thing in perpetuity or until you use EasyBCD to change the BCD again.
If, without further intervention of EasyBCD, something changes between boots, then it is "bootmgr" code which is causing the change of behaviour. (see 2 below)
In your case, switching monitors around is somehow affecting the way bootmgr behaves (accessing unchanged data in the BCD).
My system is set up to use my newest, HD monitor as my primary device, an older SD monitor as a secondary alongside and an HDTV (in another room) as a third device for movie viewing via WMC.
Owing to the vagaries of my graphics card's connections mix, my "primary" monitor is not the first one detected during POST, so my BIOS flash and my boot menu pop up on the secondary monitor (which is the first GCU channel detected) until such time as my Windows "preferences" can be determined (at desktop initiation), at which point everything flips across from the old monitor to the new. (6 below)
I don't know why "metro" is sensitive to the h/w switching particularly, never having bothered with it. Since it's only present for two seconds each IPL, I don't give a fig what it looks like, as long as I retain the ability to jump in and change my boot choice once a month.
1.After pressing the power button, the PC’s firmware initiates a Power-On Self Test (POST) and loads firmware settings. This pre-boot process ends when a valid system disk is detected.
2.Firmware reads the master boot record (MBR), and then starts Bootmgr.exe. Bootmgr.exe finds and starts the Windows loader (Winload.exe) on the Windows boot partition.
3.Essential drivers required to start the Windows kernel are loaded and the kernel starts to run, loading into memory the system registry hive and additional drivers that are marked as BOOT_START.
4.The kernel passes control to the session manager process (Smss.exe) which initializes the system session, and loads and starts the devices and drivers that are not marked BOOT_START.
5.Winlogon.exe starts, the user logon screen appears, the service control manager starts services, and any Group Policy scripts are run. When the user logs in, Windows creates a session for that user.
6.Explorer.exe starts, the system creates the desktop window manager (DWM) process, which initializes the desktop and displays it.