Okay, I've found a workaround.
After applying the proposed patch found on 
http://markmail.org/message/bildjl47nchykx3i it seems to work perfectly:
--- a/drivers/ata/pata_via.c    2009-01-16 02:36:58.000000000 +0800
+++ a/drivers/ata/pata_via.c    2009-01-16 02:39:04.000000000 +0800
@@ -347,12 +347,11 @@
  */
 static void via_tf_load(struct ata_port *ap, const struct ata_taskfile *tf)
 {
-       struct ata_taskfile tmp_tf;
+       struct ata_ioports *ioaddr = &ap->ioaddr;

-       if (ap->ctl != ap->last_ctl && !(tf->flags & ATA_TFLAG_DEVICE)) {
-               tmp_tf = *tf;
-               tmp_tf.flags |= ATA_TFLAG_DEVICE;
-               tf = &tmp_tf;
+       if (tf->ctl != ap->last_ctl) {
+               iowrite8(tf->ctl, ioaddr->ctl_addr);
+               iowrite8(tf->device, ioaddr->device_addr);

-- 
pata_via can't access 2nd SATA HDD (err_mask=0x1)
https://bugs.launchpad.net/bugs/356139
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