I have a similar problem in a related but different situation. My
experience doesn't quite help you with the specific investigation of
this case but may serve as a weak confirmation that this is indeed a
kernel issue.

Similarities
* same hardware: ThinkPad X220 Tablet with an Ultrabase docking station; the 
tablet doesn't make a difference wrt. docking
* same symptoms: disk not recognized

Differences:
* I'm running Gentoo Linux with kernel 3.4.11 (original version plus a few 
Gentoo-specific patches, i.e. the package gentoo-sources) vs. 3.6.1.
* I think connecting a USB hard disk to the docking station worked with both 
kernels, but what stopped working in my case is attaching a hard disk via the 
SATA to Ultrabay adapter.

With kernel 3.4.11 I get the following log messages:

Oct 10 18:35:15 CLANGE-x220t kernel: [ 4301.613989] ACPI: \_SB_.PCI0.SAT1.PRT1 
- docking
Oct 10 18:35:18 CLANGE-x220t kernel: [ 4305.356799] ata2: SATA link up 3.0 Gbps 
(SStatus 123 SControl 300)
Oct 10 18:35:18 CLANGE-x220t kernel: [ 4305.359664] ata2.00: ACPI cmd 
ef/02:00:00:00:00:a0 (SET FEATURES) succeeded
Oct 10 18:35:18 CLANGE-x220t kernel: [ 4305.359675] ata2.00: ACPI cmd 
f5/00:00:00:00:00:a0 (SECURITY FREEZE LOCK) filtered out
Oct 10 18:35:18 CLANGE-x220t kernel: [ 4305.362030] ata2.00: ATA-8: 
ST9500420ASG, 0002SDM1, max UDMA/133
Oct 10 18:35:18 CLANGE-x220t kernel: [ 4305.362039] ata2.00: 976773168 sectors, 
multi 16: LBA48 NCQ (depth 31/32)
Oct 10 18:35:18 CLANGE-x220t kernel: [ 4305.365187] ata2.00: ACPI cmd 
ef/02:00:00:00:00:a0 (SET FEATURES) succeeded
Oct 10 18:35:18 CLANGE-x220t kernel: [ 4305.365190] ata2.00: ACPI cmd 
f5/00:00:00:00:00:a0 (SECURITY FREEZE LOCK) filtered out
Oct 10 18:35:18 CLANGE-x220t kernel: [ 4305.367510] ata2.00: configured for 
UDMA/133
Oct 10 18:35:19 CLANGE-x220t kernel: [ 4305.378761] ata2: EH complete
Oct 10 18:35:19 CLANGE-x220t kernel: [ 4305.378890] scsi 1:0:0:0: Direct-Access 
    ATA      ST9500420ASG     0002 PQ: 0 ANSI: 5
Oct 10 18:35:19 CLANGE-x220t kernel: [ 4305.379009] sd 1:0:0:0: [sdb] 976773168 
512-byte logical blocks: (500 GB/465 GiB)
Oct 10 18:35:19 CLANGE-x220t kernel: [ 4305.379052] sd 1:0:0:0: [sdb] Write 
Protect is off
Oct 10 18:35:19 CLANGE-x220t kernel: [ 4305.379055] sd 1:0:0:0: [sdb] Mode 
Sense: 00 3a 00 00
Oct 10 18:35:19 CLANGE-x220t kernel: [ 4305.379072] sd 1:0:0:0: [sdb] Write 
cache: enabled, read cache: enabled, doesn't support DPO or FUA
Oct 10 18:35:19 CLANGE-x220t kernel: [ 4305.379206] sd 1:0:0:0: Attached scsi 
generic sg1 type 0
Oct 10 18:35:19 CLANGE-x220t kernel: [ 4305.405429]  sdb: sdb1 sdb2
Oct 10 18:35:19 CLANGE-x220t kernel: [ 4305.405788] sd 1:0:0:0: [sdb] Attached 
SCSI disk

But with 3.6.1:

Oct 10 17:21:00 CLANGE-x220t kernel: [63577.233313] ACPI: \_SB_.PCI0.SAT1.PRT1 
- docking
<and then nothing else happens>

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https://bugs.launchpad.net/bugs/1052064

Title:
  External USB hard disks are not seen when connected to docking station

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