Comment 72 for bug 119730

Just to add some more anaylsis results to narrow this issue down:

Removing "all_generic_ide" from grub, and enforcing use of sata_uli (over ahci) by explicitly adding sata_uli to /etc/modules (and calling "update-initramfs") did the trick for me:

$ sudo hdparm -tT /dev/sda

/dev/sda:
 Timing cached reads: 1790 MB in 2.00 seconds = 895.06 MB/sec
 Timing buffered disk reads: 228 MB in 3.02 seconds = 75.39 MB/sec

$ sudo hdparm -tT /dev/sdb

/dev/sdb:
 Timing cached reads: 1892 MB in 2.00 seconds = 946.23 MB/sec
 Timing buffered disk reads: 226 MB in 3.01 seconds = 74.98 MB/sec

dmesg extract:
...
[ 16.715632] libata version 3.00 loaded.
[ 16.716662] sata_uli 0000:00:12.1: version 1.3
[ 16.716674] ACPI: PCI Interrupt 0000:00:12.1[A] -> GSI 19 (level, low) -> IRQ 19
[ 16.716788] scsi0 : sata_uli
[ 16.716841] scsi1 : sata_uli
[ 16.716968] ata1: SATA max UDMA/133 cmd 0xec00 ctl 0xe080 bmdma 0xd880 irq 19
[ 16.716971] ata2: SATA max UDMA/133 cmd 0xe000 ctl 0xdc00 bmdma 0xd888 irq 19
[ 17.180710] ata1: SATA link up 1.5 Gbps (SStatus 113 SControl 300)
[ 17.230594] ata1.00: ATA-7: ST3320620AS, 3.AAE, max UDMA/133
[ 17.230598] ata1.00: 625142448 sectors, multi 16: LBA48 NCQ (depth 0/32)
[ 17.297117] ata1.00: configured for UDMA/133
[ 17.762934] ata2: SATA link up 1.5 Gbps (SStatus 113 SControl 300)
[ 17.813154] ata2.00: ATA-7: ST3320620AS, 3.AAE, max UDMA/133
[ 17.813157] ata2.00: 625142448 sectors, multi 16: LBA48 NCQ (depth 0/32)
[ 17.879691] ata2.00: configured for UDMA/133
[ 17.879868] scsi 0:0:0:0: Direct-Access ATA ST3320620AS 3.AA PQ: 0 ANSI: 5
[ 17.879991] scsi 1:0:0:0: Direct-Access ATA ST3320620AS 3.AA PQ: 0 ANSI: 5
...
[ 19.703935] ahci 0000:03:00.0: AHCI 0001.0000 32 slots 1 ports 3 Gbps 0x1 imp
l SATA mode
[ 19.703940] ahci 0000:03:00.0: flags: 64bit ncq pm led clo pmp pio slum part
[ 19.703945] PCI: Setting latency timer of device 0000:03:00.0 to 64
[ 19.704033] scsi2 : ahci
[ 19.704090] ata3: SATA max UDMA/133 abar m8192@0xfd800000 port 0xfd800100 irq 35
[ 20.342837] ata3: SATA link up 1.5 Gbps (SStatus 113 SControl 300)
[ 20.385098] ata3.00: ATA-7: ST3500630AS, 3.AAK, max UDMA/133
[ 20.385100] ata3.00: 976773168 sectors, multi 16: LBA48 NCQ (depth 31/32)
[ 20.443318] ata3.00: configured for UDMA/133
[ 20.443513] scsi 2:0:0:0: Direct-Access ATA ST3500630AS 3.AA PQ: 0 ANSI: 5
...

So there still seems to be a bug in the libata ahci driver 2.6.24-19.41 with the second port of SATA chipsets, as both the ULi and JMicron (JMicron 20360/20363 AHCI Controller [197b:2360] (rev 02)) chipsets on my ASRock 939Dual show no trouble at all with the disk (sda and sdc, respectively) connected to the first port:

$ sudo hdparm -tT /dev/sdc

/dev/sdc:
 Timing cached reads: 1674 MB in 2.00 seconds = 837.13 MB/sec
 Timing buffered disk reads: 188 MB in 3.01 seconds = 62.44 MB/sec

Cheers,
Lars