I have checked the motherboard website and the bios on the board is the latest version. So I don't see the point in flashing it or am I making a misunderstanding?

Yes set to auto detect drives in the bios

The jumpers are set as master and slave. 1 master hard drive and 1 slave on IDE channel 1. DVD writer is master and DVD player is slave on IDE channel 2.

Device manager shows no errors for any hardware. When DVD player or DVD writer is not showing up in my computer it also does not show in device manager. They do not get listed with a ? or a ! also.

Do the DVD drives show in the BIOS?

Just as a test you could set all drives to Cable Select.

Re-flashing the BIOS is helpfull if the boot block was somehow corrupted.
This often is displayed in behaviors such as not detecting drives & or operating systems.
The symptoms can vary from boot to boot but mainly center on the inability to boot with various stages of BIOS failures.
Even occassionally making the Windows Logo but not much further.