Comment 8 for bug 114457

I also have this problem with jaunty/server. My workaround is to comment out the auto line for the alias and us post-up / pre-down to bring the aliases up:

auto eth0
iface eth0 inet static
  address 1.2.3.4
  broadcast 1.2.3.255
  netmask 255.255.255.0
  gateway 1.2.3.1
  post-up ifup eth0:0
  pre-down ifdown eth0:0

# no auto here!
iface eth0:0 inet static
  address 2.3.4.5
  broadcast 2.3.4.255
  netmask 255.255.255.0