Just to clarify before I'll test all of this.

* When I was using 2.4.x Kernel my HDD was on simple ATA on ide0, recognized as hda. I used ide-scsi for my cd-rom and it was detected as sr0 (it was on ide1 and my dvd-drive was also on ide1 and wasn't recognized at all. It isn't now too.)

* I don't have AHCI enabled, I have the possibility to enable it, but my HDD is set to be detected as IDE.

I'll do those dmesg on different kernels later today and post the results.

For future google-rs:

The Intel motherboard in question seems to have a Marvell ATA controller, to where the PATA drives are (can be) connected.

Vendor 11ABh Marvell Semiconductor (Was: Galileo Technology Ltd)
Device 6101h 614x SATA2 Controller
PCI Class Storage, type IDE

It seems that kernel 2.6.x "have problems" handling this.
There is an Alan Cox patch to support 88SE6101/88SE6145 but only for 2.6.19
http://lkml.org/lkml/2006/10/16/157
More ideas on this at gentoo-wiki:
http://gentoo-wiki.com/HARDWARE_Intel_DG965MQMKR

I've just built a 2.6.20-pre7 kernel, and it sees the LG DVD writer as sr0, also successfully burnt some DVD-s.