Just though I would add a comment that I am also seeing this behaviour. It 
(might) be related to having a "post-up" command attached to the ethernet 
configuration. Here is my interfaces file:
xfers ~ # cat /etc/network/interfaces 
# This file describes the network interfaces available on your system
# and how to activate them. For more information, see interfaces(5).

# The loopback network interface
auto lo
iface lo inet loopback

# The primary network interface
auto bond0
iface bond0 inet static
        address 172.16.1.10
        netmask 255.255.255.0
        broadcast 172.16.1.255
        network 172.16.1.0
        gateway 172.16.1.1
        dns-nameservers 10.0.0.120 10.0.1.120
        dns-search mps.lan wilts.mps.lan
        dns-domain mps.lan
        bond-slaves none
        bond_mode 802.3ad
        bond_miimon 40
        bond_lacp_rate 1
        bond_use_carrier 1
        post-up /usr/local/sbin/check-bond.sh $IFACE
        pre-down /usr/local/sbin/check-bond.sh stop $IFACE
        ## ftp.mps.lan - for internal access
        up ip addr add 172.16.1.20/24 dev $IFACE

        ## ftp-sohonet.mps.lan - for FTP/Aspera Connect over Sohonet
        up ip addr add 172.16.1.21/24 dev $IFACE
        ## ftp-abovenet-7a.mps.lan - for FTP/Aspera Connect over the Abovenet 
7A link
        up ip addr add 172.16.1.22/24 dev $IFACE
        ## ftp-abovenet-7a.mps.lan - for FTP/Aspera Connect over the Abovenet 
7B link
        up ip addr add 172.16.1.23/24 dev $IFACE

        ## faspex-sohonet.mps.lan - for FASPEX over Sohonet
        up ip addr add 172.16.1.24/24 dev $IFACE
        ## faspex-sohonet.mps.lan - for FASPEX over the Abovenet 7A link
        up ip addr add 172.16.1.25/24 dev $IFACE
        ## faspex-sohonet.mps.lan - for FASPEX over the Abovenet 7B link
        up ip addr add 172.16.1.26/24 dev $IFACE

# Slave Definition for bond0
auto eth2
iface eth2 inet manual
        bond-master bond0
        bond-primary eth2 eth3
auto eth3
iface eth3 inet manual
        bond-master bond0
        bond-primary eth2 eth3

If I comment out my post-up line, I appear to get a reliable network
interface brought up at boot time, however, with the post-up line
enabled, I often see one of the slaves fail on boot.

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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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