I am using Fedora 19 and configured the bridge when my "NetworkManager" is enabled. I am configuring the VPN through "NetworkManager", so I have to keep it on. Here is the configuration from my test system which is working absolutely fine.
# brctl show
bridge name bridge id STP enabled interfaces
br0 0080.5c260a8373dd no em1
virbr0 8000.5254004f366e yes virbr0-nic
# cat /etc/sysconfig/network-scripts/ifcfg-em1
# Generated by dracut initrd
DEVICE="em1"
ONBOOT=yes
UUID="61632098-7161-42da-b97f-9e60148f589c"
BOOTPROTO="dhcp"
HWADDR="xx:xx:xx:xx:xx:xx"
TYPE=Ethernet
NAME="em1"
BRIDGE="br0"
# cat /etc/sysconfig/network-scripts/ifcfg-br0
DEVICE="br0"
BOOTPROTO="dhcp"
TYPE="Bridge"
HWADDR="xx:xx:xx:xx:xx:xx"
MTU=9000
ONBOOT="yes"
# systemctl status NetworkManager.service
NetworkManager.service - Network Manager
Loaded: loaded (/usr/lib/systemd/system/NetworkManager.service; enabled)
Active: active (running) since Wed 2013-08-07 10:21:41 IST; 15min ago
Main PID: 736 (NetworkManager)
CGroup: name=systemd:/system/NetworkManager.service
├─ 736 /usr/sbin/NetworkManager --no-daemon
└─1165 /sbin/dhclient -d -sf /usr/libexec/nm-dhcp-client.action -pf /var/run/dhclient-br0.pid -lf /var/lib/NetworkManager/dhclient-d2d68553-f97e-7549-7a26-b34a26f29318-br0.lease -cf /var/lib/Ne...
Aug 07 10:21:56 fedora.virt NetworkManager[736]: <info> domain search '
pnq.redhat.com.'
Aug 07 10:21:56 fedora.virt NetworkManager[736]: <info> domain search '
redhat.com.'
Aug 07 10:21:56 fedora.virt NetworkManager[736]: <info> Activation (br0) Stage 5 of 5 (IPv4 Configure Commit) scheduled...
Aug 07 10:21:56 fedora.virt NetworkManager[736]: <info> Activation (br0) Stage 5 of 5 (IPv4 Commit) started...
Aug 07 10:21:57 fedora.virt NetworkManager[736]: <info> (br0): device state change: ip-config -> secondaries (reason 'none') [70 90 0]
Aug 07 10:21:57 fedora.virt NetworkManager[736]: <info> Activation (br0) Stage 5 of 5 (IPv4 Commit) complete.
Aug 07 10:21:57 fedora.virt NetworkManager[736]: <info> (br0): device state change: secondaries -> activated (reason 'none') [90 100 0]
Aug 07 10:21:57 fedora.virt NetworkManager[736]: <info> Policy set 'Bridge br0' (br0) as default for IPv4 routing and DNS.
Aug 07 10:21:57 fedora.virt NetworkManager[736]: <info> Activation (br0) successful, device activated.
This configuration will help you to configure the bridge interface over your em1 device while NetworkManager is on and also you can use the NetworkManager to configure the VPN.