The way we are doing installs on PC-BSD is to use the "MBR" loader only if the user clicks to install it from the GUI. This loads the standard freebsd /boot/boot0 MBR loader with the following command:
# gpart bootcode -b /boot/boot0 /dev/ada0
The only other time we do something like this is if you select GPT as the disk-scheme, in which case we load the protective MBR:
# gpart bootcode -b /boot/pmbr /dev/ada0
Do you remember when you did the install if you chose to use the GPT scheme? That would make a huge difference here I'm sure.
Also, we do still have the EasyBCD section in our handbook:
Dual Booting - PC-BSD Wiki