Like I told you, the file system becomes corrupt when DMA is enabled. DMA makes the hard-disk much faster, but apparently the Linux driver for the sis5513 chip has problems with this. I tested this, from a Live boot CD(/USB) with
e2fsck -f /dev/sda1
When DMA is enabled and there is a file system on it, I always got errors. If you press ctrl-c with the first error, nothing will be changed.
I disabled DMA with the kernel option
In Debian, you can do that -after booting- by going to your choice (of installation), pressing TAB, and then adding "libata.dma=0" after "-- quiet". Then return to the menu.
I noticed that after reboot this setting is not automatically put into GRUB, so first GRUB needs to be configured with "e" (edit), and putting "libata.dma=0" after "quiet". Once that has been done it's possible to boot with F10.
After booting it also needs to be changed in GRUB, so that it doesn't need to be configured again the next time you boot. You can do that in the file /etc/default/grub.
Remember this also needs to be done with live-CD's of live-USB's if you want to access the disk.