In any case, let's deal with the (main) problem.  When eth0 is not mentioned in /e/n/i, NM should configure it regardless of the "managed" setting.  But in Frank's case that doesn't happen.  In Frank's log (NM 0.9.4.0-0ubuntu4.1) we see:

Jun 26 13:50:17 zwaluw NetworkManager[1772]: <info> (eth0): carrier is OFF
Jun 26 13:50:17 zwaluw NetworkManager[1772]: <info> (eth0): new Ethernet device (driver: 'atl1c' ifindex: 2)
Jun 26 13:50:17 zwaluw NetworkManager[1772]: <info> (eth0): exported as /org/freedesktop/NetworkManager/Devices/1
Jun 26 13:50:17 zwaluw NetworkManager[1772]: <info> (eth0): now managed
Jun 26 13:50:17 zwaluw NetworkManager[1772]: <info> (eth0): device state change: unmanaged -> unavailable (reason 'managed') [10 20 2]
Jun 26 13:50:17 zwaluw NetworkManager[1772]: <info> (eth0): bringing up device.
Jun 26 13:50:17 zwaluw NetworkManager[1772]: <info> (eth0): carrier now ON (device state 20)
Jun 26 13:50:17 zwaluw NetworkManager[1772]: <info> (eth0): preparing device.
Jun 26 13:50:17 zwaluw NetworkManager[1772]: <info> (eth0): deactivating device (reason 'managed') [2]
Jun 26 13:50:17 zwaluw kernel: [   24.667139] atl1c 0000:05:00.0: irq 57 for MSI/MSI-X
Jun 26 13:50:17 zwaluw kernel: [   24.667253] atl1c 0000:05:00.0: atl1c: eth0 NIC Link is Up<100 Mbps Full Duplex>
Jun 26 13:50:17 zwaluw NetworkManager[1772]: <info> (eth0): device state change: unavailable -> disconnected (reason 'none') [20 30 0]

For comparison, here's what I see on my laptop where eth0 gets configured by NM quantal (0.9.4.0+git201206081144.2efeac8-0ubuntu1):

Jun 28 10:03:40 tenerife kernel: [   23.112806] e1000e 0000:00:19.0: irq 43 for MSI/MSI-X
Jun 28 10:03:40 tenerife kernel: [   23.113317] ADDRCONF(NETDEV_UP): eth0: link is not ready
Jun 28 10:03:40 tenerife kernel: [   23.113549] ADDRCONF(NETDEV_UP): eth0: link is not ready
[...]
Jun 28 10:03:44 tenerife NetworkManager[1017]: <info> (eth0): carrier now ON (device state 20)
Jun 28 10:03:44 tenerife NetworkManager[1017]: <info> (eth0): device state change: unavailable -> disconnected (reason 'carrier-changed') [20 30 40]
Jun 28 10:03:44 tenerife NetworkManager[1017]: <info> Auto-activating connection 'Wired connection 1'.
Jun 28 10:03:44 tenerife NetworkManager[1017]: <info> Activation (eth0) starting connection 'Wired connection 1'
Jun 28 10:03:44 tenerife NetworkManager[1017]: <info> (eth0): device state change: disconnected -> prepare (reason 'none') [30 40 0]
Jun 28 10:03:44 tenerife NetworkManager[1017]: <info> Activation (eth0) Stage 1 of 5 (Device Prepare) scheduled...
Jun 28 10:03:44 tenerife NetworkManager[1017]: <info> Activation (eth0) Stage 1 of 5 (Device Prepare) started...
Jun 28 10:03:44 tenerife NetworkManager[1017]: <info> Activation (eth0) Stage 2 of 5 (Device Configure) scheduled...
Jun 28 10:03:44 tenerife NetworkManager[1017]: <info> Activation (eth0) Stage 1 of 5 (Device Prepare) complete.
Jun 28 10:03:44 tenerife NetworkManager[1017]: <info> Activation (eth0) Stage 2 of 5 (Device Configure) starting...
Jun 28 10:03:44 tenerife NetworkManager[1017]: <info> (eth0): device state change: prepare -> config (reason 'none') [40 50 0]
Jun 28 10:03:44 tenerife NetworkManager[1017]: <info> Activation (eth0) Stage 2 of 5 (Device Configure) successful.
Jun 28 10:03:44 tenerife NetworkManager[1017]: <info> Activation (eth0) Stage 3 of 5 (IP Configure Start) scheduled.
Jun 28 10:03:44 tenerife NetworkManager[1017]: <info> Activation (eth0) Stage 2 of 5 (Device Configure) complete.
Jun 28 10:03:44 tenerife NetworkManager[1017]: <info> Activation (eth0) Stage 3 of 5 (IP Configure Start) started...
Jun 28 10:03:44 tenerife NetworkManager[1017]: <info> (eth0): device state change: config -> ip-config (reason 'none') [50 70 0]
Jun 28 10:03:44 tenerife kernel: [   26.785345] e1000e: eth0 NIC Link is Up 1000 Mbps Full Duplex, Flow Control: Rx/Tx
Jun 28 10:03:44 tenerife NetworkManager[1017]: <info> Activation (eth0) Beginning DHCPv4 transaction (timeout in 45 seconds)
Jun 28 10:03:44 tenerife kernel: [   26.785772] ADDRCONF(NETDEV_CHANGE): eth0: link becomes ready
Jun 28 10:03:44 tenerife NetworkManager[1017]: <info> dhclient started with pid 1871
Jun 28 10:03:44 tenerife NetworkManager[1017]: <info> Activation (eth0) Beginning IP6 addrconf.
Jun 28 10:03:44 tenerife dhclient: Internet Systems Consortium DHCP Client 4.1-ESV-R4
Jun 28 10:03:44 tenerife dhclient: Copyright 2004-2011 Internet Systems Consortium.
Jun 28 10:03:44 tenerife dhclient: All rights reserved.
Jun 28 10:03:44 tenerife dhclient: For info, please visit https://www.isc.org/software/dhcp/
Jun 28 10:03:44 tenerife dhclient:
Jun 28 10:03:44 tenerife NetworkManager[1017]: <info> Activation (eth0) Stage 3 of 5 (IP Configure Start) complete.
Jun 28 10:03:44 tenerife NetworkManager[1017]: <info> (eth0): DHCPv4 state changed nbi -> preinit
Jun 28 10:03:44 tenerife dhclient: Listening on LPF/eth0/f0:de:f1:6b:22:bf
Jun 28 10:03:44 tenerife dhclient: Sending on   LPF/eth0/f0:de:f1:6b:22:bf
Jun 28 10:03:44 tenerife dhclient: Sending on   Socket/fallback
Jun 28 10:03:44 tenerife dhclient: DHCPDISCOVER on eth0 to 255.255.255.255 port 67 interval 3
[...]