I don't really have any good ideas for you. From everything you describe it sounds like you are having issues with your new IDE controller and its interaction with your drive, particularly with DMA mode. The problems show up in DMA mode, but not PIO, and you only have Multi-Word DMA 2 enabled even though the drive can support Ultra DMA 2.
First make sure your IDE ribbon cable is properly seated at both ends and that you have the master/slave jumper setting configured correctly. Then go through all of the steps in the DMA problems FAQ:
Check the BIOS settings for the drive's transfer mode. Usually "Auto Detect" works best.
Try putting the drive on as master on its own channel (presumably secondary master) if it is not already on its own.
Make sure all patches for your OS are installed. Consider upgrading the BIOS of your mother board if a newer version is available.
Try the drive in another system to make sure that the problem really is with the new motherboard and system, and not just bad luck with the burner that happened to coincide with installation in the new system.