The eSATA includes a port multiplier:
Apr 17 14:05:41 Tower kernel: ata1.15: Port Multiplier 1.2, 0x197b:0x0562 r0, 2 ports, feat 0x5/0xf
That's my guess on what's causing the problems, not even sure the onboard AMD SATA controller suports port multipliers, Intel doesn't.