Both you and me we do have new mobos. Yours is decent Intel piece, mine
decent AMD one. One clue more to look for problem source on operating
system's side.

 Dont worry about system boot upon GRUB_CMDLINE_LINUX... change. You can
always play with kernel options at boot time and revert changes.

"8250.nr_uarts=5" is used by me to limit unnecessary memory occupation by 
inexsisting ports. Standard 3.x.x  kernel reserves room for 32 uarts, often 
invain.
You can limit the number by this option or leave 32 as it is.

I see IRQ 17 is shared between modem and sound card. Try to switch off
audio in BIOS or pull out of the slot if it is a card.

What I found most interesting is that IRQ 17 appears in /proc/interrupts
only while using minicom. It should be there or missing all the time,
AFAIK

Kernel complains about "nobody cares IRQ 17" shall be displayed on every
console, even prior to any login action. This is a critical system
message and as such is broadcasted ( as ordered by syslog.conf ).

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

Title:
  Serial port ttyS4 doesn't work in 12.04

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