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I have a D945GSEJT board, BIOS updated to JT0029, SATA controller set to AHCI mode. It's running Linux (Debian sid), kernel 2.6.30, but the SATA controller is only operating in 1.5 Gb/s mode, which is insufficient for high-end SSDs.
Board description says there are 2 3.0 Gb/s SATA ports http://www.intel.com/products/desktop/motherboards/D945GSEJT/D945GSEJT-overview.htm
If I understood correctly, the board uses the 945GSE Express chipset with the 82801GBM (ICH7-M) I/O controller, but the data sheet for the ICH7 family says that 3.0 Gb/s is only supported on the Desktop variant (which does not include ICH7-M) http://www.intel.com/design/chipsets/datashts/307013.htm page 191, so there seem to be two contradicting statements about 3.0 Gb/s capability.
Kernel log from the ahci driver:
[ 5.648074] ahci 0000:00:1f.2: version 3.0 [ 5.648119] ahci 0000:00:1f.2: PCI INT B -> GSI 19 (level, low) -> IRQ 19 [ 5.648320] ahci 0000:00:1f.2: irq 29 for MSI/MSI-X [ 5.648553] ahci 0000:00:1f.2: AHCI 0001.0100 32 slots 4 ports 1.5 Gbps 0x5 impl SATA mode [ 5.648668] ahci 0000:00:1f.2: flags: 64bit ncq led clo pio slum part [ 5.648754] ahci 0000:00:1f.2: setting latency timer to 64
The disk works properly in 3.0 Gb/s mode a different machine with an ICH9 based board and same kernel.