Hi,

This motherboard has 3 serial pors:
COM0 as header from WPCM450
COM1 which is internally connected as SOL (Serial-Over-LAN)
COM2 Fast 16550 UART COM port on the I/O back panel from S1260 as a PCI device.

COM0/1 are working:
com0 at isa0 port 0x3f8/8 irq 4: ns16550a, 16 byte fifo
com1 at isa0 port 0x2f8/8 irq 3: ns16550a, 16 byte fifo
com1: console

COM2 is not working:
"Intel Atom S1200 UART" rev 0x01 at pci0 dev 20 function 0 not configured

 # pcidump -v
 0:20:0: Intel Atom S1200 UART
        0x0000: Vendor ID: 8086 Product ID: 0c5f
        0x0004: Command: 0107 Status: 0010
        0x0008: Class: 07 Subclass: 00 Interface: 02 Revision: 01
0x000c: BIST: 00 Header Type: 00 Latency Timer: 00 Cache Line Size: 00
        0x0010: BAR io addr: 0x0000f000/0x0008
        0x0014: BAR mem 32bit addr: 0xfe480000/0x00000100
        0x0018: BAR empty (00000000)
        0x001c: BAR empty (00000000)
        0x0020: BAR empty (00000000)
        0x0024: BAR empty (00000000)
        0x0028: Cardbus CIS: 00000000
        0x002c: Subsystem Vendor ID: 15d9 Product ID: 0651
        0x0030: Expansion ROM Base Address: 00000000
        0x0038: 00000000
        0x003c: Interrupt Pin: 01 Line: 07 Min Gnt: 00 Max Lat: 00
        0x0040: Capability 0x05: Message Signaled Interrupts (MSI)
        0x0050: Capability 0x01: Power Management

I found a dmesg from NetBSD[1]:

puc0 at pci0 dev 20 function 0: Intel S1200 UART (com)
com2 at puc0 port 0 (16550-compatible): ioaddr 0xf000, interrupting at ioapic0 pin 16
com2: ns16550a, working fifo
com2: console

If it would help I can boot FreeBSD or Linux(Debian?).

[1] http://dmesgd.nycbug.org/index.cgi?action=dmesgd&do=view&id=2549

dmesg is from GENERIC.MP with option XHCI_DEBUG because of a problem with usb3

OpenBSD 5.8-current (XHCI_DEBUG.MP) #0: Fri Aug 21 22:26:33 EEST 2015
    vl...@ns.bsdbg.net:/sys/arch/amd64/compile/XHCI_DEBUG.MP
real mem = 4261285888 (4063MB)
avail mem = 4128247808 (3937MB)
mpath0 at root
scsibus0 at mpath0: 256 targets
mainbus0 at root
bios0 at mainbus0: SMBIOS rev. 2.7 @ 0xe9510 (23 entries)
bios0: vendor American Megatrends Inc. version "1.1" date 04/29/2014
bios0: Supermicro X9SBAA
acpi0 at bios0: rev 2
acpi0: sleep states S0 S5
acpi0: tables DSDT FACP APIC FPDT MCFG HPET SPMI EINJ ERST HEST BERT
acpi0: wakeup devices PRP4(S1)
acpitimer0 at acpi0: 3579545 Hz, 24 bits
acpimadt0 at acpi0 addr 0xfee00000: PC-AT compat
cpu0 at mainbus0: apid 0 (boot processor)
cpu0: Intel(R) Atom(TM) CPU S1260 @ 2.00GHz, 1995.22 MHz
cpu0: FPU,VME,DE,PSE,TSC,MSR,PAE,MCE,CX8,APIC,SEP,MTRR,PGE,MCA,CMOV,PAT,PSE36,CFLUSH,DS,ACPI,MMX,FXSR,SSE,SSE2,SS,HTT,TM,PBE,
SSE3,DTES64,MWAIT,DS-CPL,VMX,EST,TM2,SSSE3,CX16,xTPR,PDCM,MOVBE,NXE,LONG,LAHF,PERF,ITSC,SENSOR,ARAT
cpu0: 512KB 64b/line 8-way L2 cache
cpu0: smt 0, core 0, package 0
mtrr: Pentium Pro MTRR support, 7 var ranges, 88 fixed ranges
cpu0: apic clock running at 99MHz
cpu0: mwait min=64, max=64, C-substates=0.2.2.0.2.0.3, IBE
cpu1 at mainbus0: apid 1 (application processor)
cpu1: Intel(R) Atom(TM) CPU S1260 @ 2.00GHz, 1995.00 MHz
cpu1: FPU,VME,DE,PSE,TSC,MSR,PAE,MCE,CX8,APIC,SEP,MTRR,PGE,MCA,CMOV,PAT,PSE36,CFLUSH,DS,ACPI,MMX,FXSR,SSE,SSE2,SS,HTT,TM,PBE,
SSE3,DTES64,MWAIT,DS-CPL,VMX,EST,TM2,SSSE3,CX16,xTPR,PDCM,MOVBE,NXE,LONG,LAHF,PERF,ITSC,SENSOR,ARAT
cpu1: 512KB 64b/line 8-way L2 cache
cpu1: smt 0, core 1, package 0
ioapic0 at mainbus0: apid 2 pa 0xfec00000, version 20, 24 pins
acpimcfg0 at acpi0 addr 0xc0000000, bus 0-255
acpihpet0 at acpi0: 14318179 Hz
acpiprt0 at acpi0: bus 0 (PCI0)
acpiprt1 at acpi0: bus 1 (PRP1)
acpiprt2 at acpi0: bus 2 (PRP2)
acpiprt3 at acpi0: bus 4 (P3P4)
acpicpu0 at acpi0: C1(1000@20 halt), PSS
acpicpu1 at acpi0: C1(1000@20 halt), PSS
acpitz0 at acpi0: critical temperature is 127 degC
acpitz1 at acpi0: critical temperature is 175 degC
acpibtn0 at acpi0: SLPB
acpibtn1 at acpi0: PWRB
ipmi at mainbus0 not configured
cpu0: Enhanced SpeedStep 1995 MHz: speeds: 2000, 1900, 1800, 1700, 1600, 1500, 1400, 1300, 1200, 1100, 1000, 900, 800, 700, 6
00 MHz
pci0 at mainbus0 bus 0
pchb0 at pci0 dev 0 function 0 "Intel Atom S1260 Host" rev 0x01
ppb0 at pci0 dev 1 function 0 "Intel Atom S1200 PCIE" rev 0x01
pci1 at ppb0 bus 1
ahci0 at pci1 dev 0 function 0 "Marvell 88SE9230 AHCI" rev 0x10: msi, AHCI 1.2
ahci0: port 0: 6.0Gb/s
ahci0: port 2: 3.0Gb/s
ahci0: port 7: 1.5Gb/s
scsibus1 at ahci0: 32 targets
sd0 at scsibus1 targ 0 lun 0: <ATA, ST3160316AS, JC4B> SCSI3 0/direct fixed naa.5000c50040390431
sd0: 152627MB, 512 bytes/sector, 312581808 sectors
sd1 at scsibus1 targ 2 lun 0: <ATA, HDT722516DLA380, V43O> SCSI3 0/direct fixed naa.5000cca205ddd62d
sd1: 157066MB, 512 bytes/sector, 321672960 sectors
uk0 at scsibus1 targ 7 lun 0: <Marvell, Console, 1.01> ATAPI 3/processor removable
ppb1 at pci0 dev 2 function 0 "Intel Atom S1200 PCIE" rev 0x01
pci2 at ppb1 bus 2
xhci0 at pci2 dev 0 function 0 "Renesas uPD720201 xHCI" rev 0x03: msi
xhci0: xHCI version 1.0
xhci0: CAPLENGTH=0x20
xhci0: DOORBELL=0x800
xhci0: RUNTIME=0x600
xhci0: 64 bytes context
xhci0: supported page size 0x00000001
xhci0: 8 ports and 32 slots
xhci0: 4 scratch pages
usb0 at xhci0: USB revision 3.0
uhub0 at usb0 "Renesas xHCI root hub" rev 3.00/1.00 addr 1
xhci0: DCBAAP=00xbfd30000
xhci0: CRCR=00 (00000000bfd31000)
xhci0: ERSTBA=00xbed0d000
xhci0: ERDP=00xbfd32000
xhci0: USBCMD=0x5
xhci0: IMAN=0x2
ppb2 at pci0 dev 3 function 0 "Intel Atom S1200 PCIE" rev 0x01
pci3 at ppb2 bus 3
ppb3 at pci3 dev 0 function 0 "Newbridge PEB383 PCIE-PCI" rev 0x01
pci4 at ppb3 bus 4
em0 at pci4 dev 0 function 0 "Intel 82540EM" rev 0x02: apic 2 int 21, address 00:07:e9:10:32:a8
vga1 at pci4 dev 3 function 0 "Matrox MGA G200eW" rev 0x0a
wsdisplay0 at vga1 mux 1: console (80x25, vt100 emulation)
wsdisplay0: screen 1-5 added (80x25, vt100 emulation)
ppb4 at pci0 dev 4 function 0 "Intel Atom S1200 PCIE" rev 0x01
pci5 at ppb4 bus 5
em1 at pci5 dev 0 function 0 "Intel I350" rev 0x01: msi, address 00:25:90:c6:31:70 em2 at pci5 dev 0 function 1 "Intel I350" rev 0x01: msi, address 00:25:90:c6:31:71
"Intel Atom S1200 MEI" rev 0x01 at pci0 dev 14 function 0 not configured
"Intel Atom S1200 SMBus" rev 0x01 at pci0 dev 19 function 0 not configured "Intel Atom S1200 SMBus" rev 0x01 at pci0 dev 19 function 1 not configured "Intel Atom S1200 UART" rev 0x01 at pci0 dev 20 function 0 not configured
pcib0 at pci0 dev 31 function 0 "Intel Atom S1200 ISA" rev 0x01
isa0 at pcib0
isadma0 at isa0
com0 at isa0 port 0x3f8/8 irq 4: ns16550a, 16 byte fifo
com1 at isa0 port 0x2f8/8 irq 3: ns16550a, 16 byte fifo
com1: console
pcppi0 at isa0 port 0x61
spkr0 at pcppi0
xhci0: port=5 change=0x20
xhci0: port=8 change=0x00
xhci0: port=5 change=0x20
xhci0: xhci_cmd_slot_control
xhci0: dev 1, input=0xffffff00bfd3e000 slot=0xffffff00bfd3e040 ep0=0xffffff00bfd3e080
xhci0: dev 1, setting DCBAA to 0x00000000bfd3f000
xhci_pipe_init: pipe=0xffff80000010a000 addr=0 depth=1 port=5 speed=2 dev 1 dci 1 (epAddr=0x0)
xhci0: xhci_cmd_set_address BSR=1
xhci0: xhci_cmd_set_address BSR=0
xhci0: dev 1 addr 1
uftdi0 at uhub0 port 5 configuration 1 interface 0 "FTDI FT232R USB UART" rev 2.00/6.00 addr 2
ucom0 at uftdi0 portno 1
xhci0: port=8 change=0x00
xhci0: xhci_cmd_slot_control
xhci0: dev 2, input=0xffffff00bfd41000 slot=0xffffff00bfd41040 ep0=0xffffff00bfd41080
xhci0: dev 2, setting DCBAA to 0x00000000bfd42000
xhci_pipe_init: pipe=0xffff800000111000 addr=0 depth=1 port=8 speed=2 dev 2 dci 1 (epAddr=0x0)
xhci0: xhci_cmd_set_address BSR=1
xhci0: xhci_cmd_set_address BSR=0
xhci0: dev 2 addr 2
uhidev0 at uhub0 port 8 configuration 1 interface 0 "Winbond Electronics Corp Hermon USB hidmouse Device" rev 1.10/0.01 addr
3
uhidev0: iclass 3/1
ums0 at uhidev0: 3 buttons, Z dir
wsmouse0 at ums0 mux 0
uhidev1 at uhub0 port 8 configuration 1 interface 1 "Winbond Electronics Corp Hermon USB hidmouse Device" rev 1.10/0.01 addr
3
uhidev1: iclass 3/1
ukbd0 at uhidev1: 8 variable keys, 6 key codes
xhci_pipe_init: pipe=0xffff800000114000 addr=3 depth=1 port=8 speed=2 dev 2 dci 3 (epAddr=0x81)
xhci0: xhci_cmd_configure_ep dev 2
wskbd0 at ukbd0: console keyboard, using wsdisplay0
vscsi0 at root
scsibus2 at vscsi0: 256 targets
softraid0 at root
scsibus3 at softraid0: 256 targets
sd2 at scsibus3 targ 1 lun 0: <OPENBSD, SR RAID 1, 005> SCSI2 0/direct fixed
sd2: 152625MB, 512 bytes/sector, 312576113 sectors
root on sd2a (2369b3fc45f6ff52.a) swap on sd2b dump on sd2b
xhci_pipe_init: pipe=0xffff800000a7e000 addr=2 depth=1 port=5 speed=2 dev 1 dci 3 (epAddr=0x81)
xhci0: xhci_cmd_configure_ep dev 1
xhci_pipe_init: pipe=0xffff800000a89000 addr=2 depth=1 port=5 speed=2 dev 1 dci 4 (epAddr=0x2)
xhci0: xhci_cmd_configure_ep dev 1

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