FWIW I have an MSI (P45 Neo2) mobo with JMB363 (only PATA connected)
and its second AHCI port (ata8, not connected) gives me the following.
The 2.6.26.2 kernel doesn't see any problem:
Linux version 2.6.26.2 (gcc version 4.3.0 20080428 (Red Hat 4.3.0-8) SMP
ata7: SATA max UDMA/133 abar m8192@0xfeafe000 port 0xfeafe100 irq 16
ata8: SATA max UDMA/133 abar m8192@0xfeafe000 port 0xfeafe180 irq 16
ata7: SATA link down (SStatus 0 SControl 300)
ata8: SATA link down (SStatus 0 SControl 300)
ata9: PATA max UDMA/100 cmd 0xdc00 ctl 0xd880 bmdma 0xd400 irq 17
ata10: PATA max UDMA/100 cmd 0xd800 ctl 0xd480 bmdma 0xd408 irq 17
ata9.00: ATAPI: _NEC DVD_RW ND-4550A, 1.09, max UDMA/33
ata9.00: configured for UDMA/33
Now with 2.6.26.3:
ata7: SATA max UDMA/133 abar m8192@0xfeafe000 port 0xfeafe100 irq 16
ata8: SATA max UDMA/133 abar m8192@0xfeafe000 port 0xfeafe180 irq 16
ata7: SATA link down (SStatus 0 SControl 300)
ata8: SATA link down (SStatus 0 SControl 300)
ata9: PATA max UDMA/100 cmd 0xdc00 ctl 0xd880 bmdma 0xd400 irq 17
ata10: PATA max UDMA/100 cmd 0xd800 ctl 0xd480 bmdma 0xd408 irq 17
ata9.00: ATAPI: _NEC DVD_RW ND-4550A, 1.09, max UDMA/33
ata9.00: configured for UDMA/33
ata8: exception Emask 0x10 SAct 0x0 SErr 0x4000000 action 0xe frozen
ata8: irq_stat 0x00000040, connection status changed
ata8: SError: { DevExch }
ata8: hard resetting link
ata8: SATA link down (SStatus 0 SControl 300)
ata8: EH complete
ata8: exception Emask 0x10 SAct 0x0 SErr 0x4000000 action 0xe frozen
ata8: irq_stat 0x00000040, connection status changed
ata8: SError: { DevExch }
ata8: hard resetting link
ata8: SATA link down (SStatus 0 SControl 300)
ata8: EH complete
ata8: exception Emask 0x10 SAct 0x0 SErr 0x4000000 action 0xe frozen
ata8: irq_stat 0x00000040, connection status changed
ata8: SError: { DevExch }
ata8: hard resetting link
...
.config differences which could somehow be relevant(?):
-CONFIG_GART_IOMMU=y
-CONFIG_K8_NB=y
-CONFIG_AGP_AMD64=y
(I'm using SWIOTLB in both cases, it's ...