We can confirm similar issues with Precise. However, testing a default
Precise 12.04.3 installation with any generic Quantal or Raring LTS
kernel seems to work fine.
Tests preformed:
Continues looping boot using a similar script as mentioned by Chris J Arges. 
Counted amount of successful boots - working bond0 with both slaves up - with 
different kernels.

Symptoms after boot:
- Bond0 down with no slaves
- Bond0 comes up with only 1 slave
- Bond0 comes up with 2 slaves with 1 interface marked down

Hardware:
Dell M610-II
01:00.0 Ethernet controller: Broadcom Corporation NetXtreme II BCM5709S Gigabit 
Ethernet (rev 20)
01:00.1 Ethernet controller: Broadcom Corporation NetXtreme II BCM5709S Gigabit 
Ethernet (rev 20)

Network configuration:
root@test:~# cat /etc/network/interfaces
auto lo
iface lo inet loopback

auto eth0
iface eth0 inet manual
  bond-master bond0
  bond-primary eth0 eth1

auto eth1
iface eth1 inet manual
  bond-master bond0
  bond-primary eth0 eth1

auto bond0
iface bond0 inet static
  address 10.1.1.2
  netmask 255.255.255.0
  broadcast 10.1.1.255
  gateway 10.1.1.1
  bond_arp_validate 3
  bond_mode active-backup
  bond_arp_interval 200
  bond_arp_ip_target 10.1.1.1
  bond_slaves none

root@test:~# cat /etc/modprobe.d/bonding.conf
alias bond0 bonding
options bonding mode=1 arp_interval=200 arp_ip_target=10.1.1.1

Test results:
Ubuntu 12.04.3 LTS with linux-image-3.2.0-54-generic (3.2.0-54.82) - Failed 
several boots with the listed symptoms
Ubuntu 12.04.3 LTS with linux-image-3.5.0-41-generic (3.5.0-41.64~precise1) - 
300+ boots
Ubuntu 12.04.3 LTS with linux-image-3.8.0-31-generic (3.8.0-31.46~precise1) - 
300+ boots

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https://bugs.launchpad.net/bugs/996369

Title:
  bond slave interface sometimes does not come up on boot

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