I think it's pooped out... and it only sees one.

[    5.956680] ata3: link is slow to respond, please be patient (ready=0)

[   10.970015] ata3: device not ready (errno=-16), forcing hardreset
[   16.136680] ata3: link is slow to respond, please be patient (ready=0)
[   20.990011] ata3: SRST failed (errno=-16)
[   26.156678] ata3: link is slow to respond, please be patient (ready=0)
[   31.010012] ata3: SRST failed (errno=-16)
[   36.176675] ata3: link is slow to respond, please be patient (ready=0)
[   66.043340] ata3: SRST failed (errno=-16)
[   71.050008] ata3: SRST failed (errno=-16)
[   71.061817] ata3: reset failed, giving up

This was a bit interesting though:

[    0.939779] ata1: PATA max UDMA/100 cmd 0x1f0 ctl 0x3f6 bmdma 0xffa0 irq 14

[    0.939783] ata2: PATA max UDMA/100 cmd 0x170 ctl 0x376 bmdma 0xffa8 irq 15
[    0.939875] ata1: port disabled--ignoring
[    0.943281] pata_sil680 0000:01:07.0: version 0.4.9
[    0.943325] sil680: 133MHz clock.
[    0.944316] scsi2 : pata_sil680
[    0.944507] scsi3 : pata_sil680
[    0.944666] ata3: PATA max UDMA/133 cmd 0xecf8 ctl 0xecf0 bmdma 0xecc0 irq 16
[    0.944671] ata4: PATA max UDMA/133 cmd 0xece0 ctl 0xecd8 bmdma 0xecc8 irq 16
[    0.945455] Error: Driver 'pata_platform' is already registered, aborting...

It sees the one on ata3, and read your cdrom, but the drive is stalling response, not sure that's not due to kernel oddities though at the end of that.  Check the status of the drives in the bios, it should usually register or show them in legacy bios ata devices. Can try to play with the ata modes in the bios.

Maybe try changing the modes or jumpers, maybe they're both master devices?  Mmm, master/slave jumpers, makes me feel old to remember them on drives...

Try one at a time too to rule it out, or another controller.

-mb