Hi Roger,
finally solved similar problem with my server. The solution is to add kernel 
option "PCI=routeirq" while booting (for test if works) and if it does to 
GRUB_CMDLINE_LINUX in /etc/default/grub. Then run "update-grub".

My GRUB_CMDLINE_LINUX parameter is as follows:

GRUB_CMDLINE_LINUX="8250.nr_uarts=5 PCI=routeirq"

The former kernel option limits ttySx devices to required number.

Hope this will help you.
Cheers

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https://bugs.launchpad.net/bugs/1087519

Title:
  Serial port ttyS4 doesn't work in 12.04

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