Hi there,
Is the DVD/CD Writer I am looking at the same as yours with an older IDE connector? If it is then you need to make sure that the GSATA/IDE Ctrl is enabled and the GSATA/IDE Mode is set to IDE.
It is worth noting that there have been some problems when trying to run older IDE devices alongside SATA drives and it is often easier and cheaper in the long run to replace the DVD/CD Writer with one that has a SATA interface.
As you have stated, your instability problems could be due to not doing a clean install of the OS and whenever you replace a major component, such as a motherboard, it is always best to reinstall everything so there can be no registry conflicts.