I've been following this bug since hardy.
Nowadays is only annoying sin I can boot after waiting for an extra 30 seconds  
or more without problem.
In the past I upgraded BIOS, firmwares, etc but problem remains.

My config is:
Seagate Barracuda at SATA port.
Western Digital Caviar at IDE port (master).
DVD-ROM at second IDE port (master).
DVD-ROM writer at second IDE port (slave)

The problem is shown when detecting legacy IDE units.

[    1.207345] input: AT Translated Set 2 keyboard as 
/devices/platform/i8042/serio0/input/input3
[    1.242560] ata1: SATA link up 3.0 Gbps (SStatus 123 SControl 300)
[    1.301915] ata1.00: ATA-7: ST3400833AS, 3.AAE, max UDMA/133
[    1.301982] ata1.00: 781422768 sectors, multi 16: LBA48 NCQ (depth 31/32)
[    1.393552] ata1.00: configured for UDMA/133
[    1.393719] scsi 0:0:0:0: Direct-Access     ATA      ST3400833AS      3.AA 
PQ: 0 ANSI: 5
[    1.393914] sd 0:0:0:0: Attached scsi generic sg0 type 0
[    1.394019] sd 0:0:0:0: [sda] 781422768 512-byte logical blocks: (400 GB/372 
GiB)
[    1.394141] sd 0:0:0:0: [sda] Write Protect is off
[    1.394208] sd 0:0:0:0: [sda] Mode Sense: 00 3a 00 00
[    1.394231] sd 0:0:0:0: [sda] Write cache: enabled, read cache: enabled, 
doesn't support DPO or FUA
[    1.394439]  sda:
[    1.405403] ata2: SATA link down (SStatus 0 SControl 300)
[    1.416363] ata4: SATA link down (SStatus 0 SControl 300)
[    1.433212]  sda1 sda2 sda3 sda4
[    1.451029] sd 0:0:0:0: [sda] Attached SCSI disk
[    1.560037] usb 1-7: new high speed USB device using ehci_hcd and address 3
[    1.715423] usb 1-7: configuration #1 chosen from 1 choice
[    2.052521] usb 2-1: new full speed USB device using ohci_hcd and address 2
[    2.276096] usb 2-1: configuration #1 chosen from 1 choice
[    2.279073] hub 2-1:1.0: USB hub found
[    2.282049] hub 2-1:1.0: 2 ports detected
[    2.574049] usb 2-1.1: new full speed USB device using ohci_hcd and address 3
[    2.699090] usb 2-1.1: configuration #1 chosen from 1 choice
[    2.791056] usb 2-1.2: new full speed USB device using ohci_hcd and address 4
[    2.920100] usb 2-1.2: configuration #1 chosen from 1 choice
[    6.300027] ata5: link is slow to respond, please be patient (ready=0)
[   11.160027] ata5: SRST failed (errno=-16)
[   16.360026] ata5: link is slow to respond, please be patient (ready=0)
[   21.220027] ata5: SRST failed (errno=-16)
[   26.420027] ata5: link is slow to respond, please be patient (ready=0)
[   52.220071] ata5.01: link status unknown, clearing UNKNOWN to NONE
[   52.241764] ata5.00: ATA-6: WDC WD2000JB-00GVA0, 08.02D08, max UDMA/100
[   52.241833] ata5.00: 390721968 sectors, multi 16: LBA48 
[   52.241921] ata5: nv_mode_filter: 0x3f39f&0x3f39f->0x3f39f, BIOS=0x3f000 
(0xc600c0c0) ACPI=0x3f01f (20:900:0x11)
[   52.281697] ata5.00: configured for UDMA/100
[   52.281840] scsi 4:0:0:0: Direct-Access     ATA      WDC WD2000JB-00G 08.0 
PQ: 0 ANSI: 5
[   52.282029] sd 4:0:0:0: Attached scsi generic sg1 type 0
[   52.282128] sd 4:0:0:0: [sdb] 390721968 512-byte logical blocks: (200 GB/186 
GiB)
[   52.282249] sd 4:0:0:0: [sdb] Write Protect is off
[   52.282314] sd 4:0:0:0: [sdb] Mode Sense: 00 3a 00 00
[   52.282337] sd 4:0:0:0: [sdb] Write cache: enabled, read cache: enabled, 
doesn't support DPO or FUA
[   52.282549]  sdb: sdb2 < sdb5 >
[   52.315275] sd 4:0:0:0: [sdb] Attached SCSI disk
[   52.480475] ata6.00: ATAPI: TOSHIBA DVD-ROM SD-M1402, 1010, max UDMA/33
[   52.480572] ata6.01: ATAPI: ATAPI   DVD DUAL 8X4X12, B3LC, max UDMA/33
[   52.480661] ata6: nv_mode_filter: 0x739f&0x739f->0x739f, BIOS=0x7000 
(0xc600c0c0) ACPI=0x701f (60:60:0x15)
[   52.480666] ata6: nv_mode_filter: 0x739f&0x739f->0x739f, BIOS=0x7000 
(0xc600c0c0) ACPI=0x701f (60:60:0x15)
[   52.520426] ata6.00: configured for UDMA/33
[   52.560690] ata6.01: configured for UDMA/33
[   52.565315] scsi 5:0:0:0: CD-ROM            TOSHIBA  DVD-ROM SD-M1402 1010 
PQ: 0 ANSI: 5
[   52.572871] sr0: scsi3-mmc drive: 40x/40x cd/rw xa/form2 cdda tray
[   52.572939] Uniform CD-ROM driver Revision: 3.20
[   52.573072] sr 5:0:0:0: Attached scsi CD-ROM sr0
[   52.573118] sr 5:0:0:0: Attached scsi generic sg2 type 5
[   52.575056] scsi 5:0:1:0: CD-ROM            ATAPI    DVD DUAL 8X4X12  B3LC 
PQ: 0 ANSI: 5

My hardware:
     *-ide:0
          description: IDE interface
          product: MCP51 IDE
          vendor: nVidia Corporation
          physical id: d
          bus info: p...@0000:00:0d.0
          logical name: scsi4
          logical name: scsi5
          version: a1
          width: 32 bits
          clock: 66MHz
          capabilities: ide pm bus_master cap_list emulated
          configuration: driver=pata_amd latency=0 maxlatency=1 mingnt=3
          resources: irq:0 ioport:1f0(size=8) ioport:3f6 ioport:170(size=8) 
ioport:376 ioport:ffa0(size=16)
        *-disk
             description: ATA Disk
             product: WDC WD2000JB-00G
             vendor: Western Digital
             physical id: 0
             bus info: s...@4:0.0.0
             logical name: /dev/sdb
             version: 08.0
             serial: WD-WMAL81192472
             size: 186GiB (200GB)
             capabilities: partitioned partitioned:dos
             configuration: ansiversion=5 signature=b766b766
           *-volume

-- 
Boot fails on ata3: SRST failed (errno=-16)
https://bugs.launchpad.net/bugs/220706
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